Diverse organic-mineral associations in Jezero crater, Mars.

The presence and distribution of preserved organic matter on the surface of Mars can provide key information about the Martian carbon cycle and the potential of the planet to host life throughout its history. Several types of organic molecules have been previously detected in Martian meteorites1 and at Gale crater, Mars2-4. Evaluating the diversity and detectability of organic matter elsewhere on Mars is important for understanding the extent and diversity of Martian surface processes and the potential availability of carbon sources1,5,6. Here we report the detection of Raman and fluorescence spectra consistent with several species of aromatic organic molecules in the Máaz and Séítah formations within the Crater Floor sequences of Jezero crater, Mars. We report specific fluorescence-mineral associations consistent with many classes of organic molecules occurring in different spatial patterns within these compositionally distinct formations, potentially indicating different fates of carbon across environments. Our findings suggest there may be a diversity of aromatic molecules prevalent on the Martian surface, and these materials persist despite exposure to surface conditions. These potential organic molecules are largely found within minerals linked to aqueous processes, indicating that these processes may have had a key role in organic synthesis, transport or preservation.

Simultaneous inference of parental admixture proportions and admixture times from unphased local ancestry calls.

Population genetic analyses of local ancestry tracts routinely assume that the ancestral admixture process is identical for both parents of an individual, an assumption that may be invalid when considering recent admixture. Here, we present Parental Admixture Proportion Inference (PAPI), a Bayesian tool for inferring the admixture proportions and admixture times for each parent of a single admixed individual. PAPI analyzes unphased local ancestry tracts and has two components: a binomial model that leverages genome-wide ancestry fractions to infer parental admixture proportions and a hidden Markov model (HMM) that infers admixture times from tract lengths. Crucially, the HMM accounts for unobserved within-ancestry recombination by approximating the pedigree crossover dynamics, enabling inference of parental admixture times. In simulations, we find that PAPI's admixture proportion estimates deviate from the truth by 0.047 on average, outperforming ANCESTOR and PedMix by 46.0% and 57.6%, respectively. Moreover, PAPI's admixture time estimates were strongly correlated with the truth (R=0.76) but have an average downward bias of 1.01 generations that is partly attributable to inaccuracies in local ancestry inference. As an illustration of its utility, we ran PAPI on African American genotypes from the PAGE study (N = 5,786) and found strong evidence of assortative mating by ancestry proportion: couples' ancestry proportions are highly correlated (R = 0.87) and are closer to each other than expected under random mating (p < 10-6). We anticipate that PAPI will be useful in studying the population dynamics of admixture and will also be of interest to individuals seeking to learn about their personal genealogies.

Distinguishing pedigree relationships via multi-way identity by descent sharing and sex-specific genetic maps.

The proportion of samples with one or more close relatives in a genetic dataset increases rapidly with sample size, necessitating relatedness modeling and enabling pedigree-based analyses. Despite this, relatives are generally unreported and current inference methods typically detect only the degree of relatedness of sample pairs and not pedigree relationships. We developed CREST, an accurate and fast method that identifies the pedigree relationships of close relatives. CREST utilizes identity by descent (IBD) segments shared between a pair of samples and their mutual relatives, leveraging the fact that sharing rates among these individuals differ across pedigree configurations. Furthermore, CREST exploits the profound differences in sex-specific genetic maps to classify pairs as maternally or paternally related-e.g., paternal half-siblings-using the locations of autosomal IBD segments shared between the pair. In simulated data, CREST correctly classifies 91.5%-100% of grandparent-grandchild (GP) pairs, 80.0%-97.5% of avuncular (AV) pairs, and 75.5%-98.5% of half-siblings (HS) pairs compared to PADRE's rates of 38.5%-76.0% of GP, 60.5%-92.0% of AV, 73.0%-95.0% of HS pairs. Turning to the real 20,032 sample Generation Scotland (GS) dataset, CREST identified seven pedigrees with incorrect relationship types or maternal/paternal parent sexes, five of which we confirmed as mistakes, and two with uncertain relationships. After correcting these, CREST correctly determines relationship types for 93.5% of GP, 97.7% of AV, and 92.2% of HS pairs that have sufficient mutual relative data; the parent sex in 100% of HS and 99.6% of GP pairs; and it completes this analysis in 2.8 h including IBD detection in eight threads.

Patterns of genetic connectedness between modern and medieval Estonian genomes reveal the origins of a major ancestry component of the Finnish population.

The Finnish population is a unique example of a genetic isolate affected by a recent founder event. Previous studies have suggested that the ancestors of Finnic-speaking Finns and Estonians reached the circum-Baltic region by the 1st millennium BC. However, high linguistic similarity points to a more recent split of their languages. To study genetic connectedness between Finns and Estonians directly, we first assessed the efficacy of imputation of low-coverage ancient genomes by sequencing a medieval Estonian genome to high depth (23×) and evaluated the performance of its down-sampled replicas. We find that ancient genomes imputed from >0.1× coverage can be reliably used in principal-component analyses without projection. By searching for long shared allele intervals (LSAIs; similar to identity-by-descent segments) in unphased data for >143,000 present-day Estonians, 99 Finns, and 14 imputed ancient genomes from Estonia, we find unexpectedly high levels of individual connectedness between Estonians and Finns for the last eight centuries in contrast to their clear differentiation by allele frequencies. High levels of sharing of these segments between Estonians and Finns predate the demographic expansion and late settlement process of Finland. One plausible source of this extensive sharing is the 8th-10th centuries AD migration event from North Estonia to Finland that has been proposed to explain uniquely shared linguistic features between the Finnish language and the northern dialect of Estonian and shared Christianity-related loanwords from Slavic. These results suggest that LSAI detection provides a computationally tractable way to detect fine-scale structure in large cohorts.

Haptools: a toolkit for admixture and haplotype analysis.

SUMMARY: Leveraging local ancestry and haplotype information in genome-wide association studies and downstream analyses can improve the utility of genomics for individuals from diverse and recently admixed ancestries. However, most existing simulation, visualization and variant analysis frameworks are based on variant-level analysis and do not automatically handle these features. We present haptools, an open-source toolkit for performing local ancestry aware and haplotype-based analysis of complex traits. Haptools supports fast simulation of admixed genomes, visualization of admixture tracks, simulation of haplotype- and local ancestry-specific phenotype effects and a variety of file operations and statistics computed in a haplotype-aware manner. AVAILABILITY AND IMPLEMENTATION: Haptools is freely available at https://github.com/cast-genomics/haptools. DOCUMENTATION: Detailed documentation is available at https://haptools.readthedocs.io. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Examination of protective factors that promote prosocial skill development among children exposed to intimate partner violence.

This retrospective cohort study examined prosocial skills development in child welfare-involved children, how intimate partner violence (IPV) exposure explained heterogeneity in children's trajectories of prosocial skill development, and the degree to which protective factors across children's ecologies promoted prosocial skill development. Data were from 1,678 children from the National Survey of Child and Adolescent Well-being I, collected between 1999 and 2007. Cohort-sequential growth mixture models were estimated to identify patterns of prosocial skill development between the ages of 3 to 10 years. Four diverse pathways were identified, including two groups that started high (high subtle-decreasing; high decreasing-to-increasing) and two groups that started low (low stable; low increasing-to-decreasing). Children with prior history of child welfare involvement, preschool-age IPV exposure, school-age IPV exposure, or family income below the federal poverty level had higher odds of being in the high decreasing-to-increasing group compared with the high subtle-decreasing group. Children with a mother with greater than high school education or higher maternal responsiveness had higher odds of being in the low increasing-to-decreasing group compared with the low stable group. The importance of maternal responsiveness in fostering prosocial skill development underlines the need for further assessment and intervention. Recommendations for clinical assessment and parenting programs are provided.

The Health Care Transition Needs of Adolescents and Emerging Adults with Chronic Pain: A Narrative Review.

The aim of this narrative review was to provide an overview of what is known about the health care transition process in pediatric chronic pain, barriers to successful transition of care, and the roles that pediatric psychologists and other health care providers can play in the transition process. Searches were run in in Ovid, PsycINFO, Academic Search Complete, and PubMed. Eight relevant articles were identified. There are no published protocols, guidelines, or assessment measures specific to the health care transition in pediatric chronic pain. Patients report many barriers to the transition process, including difficulty attaining reliable medical information, establishing care with new providers, financial concerns, and adapting to the increased personal responsibility for their medical care. Additional research is needed to develop and test protocols to facilitate transition of care. Protocols should emphasize structured, face-to-face interactions and include high levels of coordination between pediatric and adult care teams.

Rapid, Phase-free Detection of Long Identity-by-Descent Segments Enables Effective Relationship Classification.

Identity-by-descent (IBD) segments are a useful tool for applications ranging from demographic inference to relationship classification, but most detection methods rely on phasing information and therefore require substantial computation time. As genetic datasets grow, methods for inferring IBD segments that scale well will be critical. We developed IBIS, an IBD detector that locates long regions of allele sharing between unphased individuals, and benchmarked it with Refined IBD, GERMLINE, and TRUFFLE on 3,000 simulated individuals. Phasing these with Beagle 5 takes 4.3 CPU days, followed by either Refined IBD or GERMLINE segment detection in 2.9 or 1.1 h, respectively. By comparison, IBIS finishes in 6.8 min or 7.8 min with IBD2 functionality enabled: speedups of 805-946× including phasing time. TRUFFLE takes 2.6 h, corresponding to IBIS speedups of 20.2-23.3×. IBIS is also accurate, inferring ≥7 cM IBD segments at quality comparable to Refined IBD and GERMLINE. With these segments, IBIS classifies first through third degree relatives in real Mexican American samples at rates meeting or exceeding other methods tested and identifies fourth through sixth degree pairs at rates within 0.0%-2.0% of the top method. While allele frequency-based approaches that do not detect segments can infer relationship degrees faster than IBIS, the fastest are biased in admixed samples, with KING inferring 30.8% fewer fifth degree Mexican American relatives correctly compared with IBIS. Finally, we ran IBIS on chromosome 2 of the UK Biobank dataset and estimate its runtime on the autosomes to be 3.3 days parallelized across 128 cores.

Thymidine kinase activity levels in serum can identify HR+ metastatic breast cancer patients with a low risk of early progression (SWOG S0226).

BACKGROUND: Some patients with metastatic breast cancer (MBC) stay on endocrine therapy (ET) for years and others progress quickly. Serum thymidine kinase activity (TKa), an indicator of cell-proliferation, is a potential biomarker for monitoring ET and predicting MBC outcome. We have previously reported TKa as being prognostic in MBC in SWOG S0226. Here, new data on progression within 30/60 days post sampling, with a new, FDA approved version of DiviTum®TKa highlighting differences vs. a Research Use Only version is reported. METHODS: 1,546 serum samples from 454 patients were assessed, collected at baseline and at 4 subsequent timepoints during treatment. A new predefined cut-off tested the ability to predict disease progression. A new measuring unit, DuA (DiviTum® unit of Activity) is adopted. RESULTS: A DiviTum®TKa score <250 DuA provides a much lower risk of progression within 30/60 days after blood draw, the negative predictive value (NPV) was 96.7% and 93.5%, respectively. Patients <250 DuA experienced significantly longer progression-free survival and overall survival, demonstrated at baseline and for all time intervals. CONCLUSIONS: DiviTum®TKa provides clinically meaningful information for patients with HR+ MBC. Low TKa levels provide such a high NPV for rapid progression that such patients might forego additional therapy added to single agent ET.Trial registration: NCT00075764.

Development and Design Needs of Mobile Health (mHealth) Apps for Adolescents.

Context: Adolescent obesity remains a significant public health issue within the United States. Application (app) technology growth and popularity offer new opportunities for research and health improvement. The development of a consolidated mobile health application (mHealth app) for adolescents on these platforms has the potential to improve health outcomes. Most mHealth apps for adolescents, particularly those in the commercial arena, are scaled-down from an adult-targeted app and lack relevant stakeholder feedback. Objectives: To identify adolescent expectations when using an mHealth application and understand visual user-interface needs, and to develop an intuitive and engaging user-interface, we aim to describe the design and functional user requirements for mHealth app. We aim to inform future researchers and app developers about adolescent needs and preferences, as identified by adolescent stakeholders. Study Design: In this mixed method study, we used surveys and interviews/task analysis of adolescents to understand their user requirements and design preferences during the development of a healthy lifestyle app (CommitFit). The survey included the user design industry-standard System Usability Scale (SUS) paired with supplemental questionnaire on the specific features and functionalities of the CommitFit mHealth app. Population Studied: Adolescents ranged from the ages of 13 to 15 years of age, with an average age of 13.6 years old. Results: Ten adolescents were interviewed and surveyed (adapted SUS and supplemental questionnaire) to explore adolescent preferences with visual app design and functionality. Our qualitative results showed that adolescents preferred colorful, user-friendly interfaces paired with gamification to use an mHealth app. Our analysis of SUS survey data validated our user-centered and human-system design and adolescents confirmed their design, feature, and functionality preferences. Adolescent users found CommitFit to be easy to use and provided guidance for visual design needs and preferences. Outcomes: Adolescent stakeholder feedback is crucial in the successful development of an adolescent-targeted mHealth app. Adolescents prefer vibrant colors, modern, easy-to-use interface, gamification and rewards, customizable and personalized, simple, and mature graphics. Adolescents were especially motivated by gamification techniques in maintaining their interest in the application and their health behavior goals.

Mechanism underlying a brief cognitive behavioral treatment for head and neck cancer survivors with body image distress.

PURPOSE: Body image distress (BID) among head and neck cancer (HNC) survivors is a debilitating toxicity associated with depression, anxiety, stigma, and poor quality of life. BRIGHT (Building a Renewed ImaGe after Head & neck cancer Treatment) is a brief cognitive behavioral therapy (CBT) that reduces BID for these patients. This study examines the mechanism underlying BRIGHT. METHODS: In this randomized clinical trial, HNC survivors with clinically significant BID were randomized to receive five weekly psychologist-led video tele-CBT sessions (BRIGHT) or dose-and delivery matched survivorship education (attention control [AC]). Body image coping strategies, the hypothesized mediators, were assessed using the Body Image Coping Skills Inventory (BICSI). HNC-related BID was measured with the Inventory to Measure and Assess imaGe disturbancE-Head and Neck (IMAGE-HN). Causal mediation analyses were used to estimate the mediated effects of changes in BICSI scores on changes in IMAGE-HN scores. RESULTS: Among 44 HNC survivors with BID allocated to BRIGHT (n = 20) or AC (n = 24), mediation analyses showed that BRIGHT decreased avoidant body image coping (mean change in BICSI-Avoidance scale score) from baseline to 1-month post-intervention relative to AC (p = 0.039). Decreases in BICSI-Avoidance scores from baseline to 1-month resulted in decreases in IMAGE-HN scores from baseline to 3 months (p = 0.009). The effect of BRIGHT on IMAGE-HN scores at 3 months was partially mediated by a decrease in BICSI-Avoidance scores (p = 0.039). CONCLUSIONS: This randomized trial provides preliminary evidence that BRIGHT reduces BID among HNC survivors by decreasing avoidant body image coping. Further research is necessary to confirm these results and enhance the development of interventions targeting relevant pathways to reduce BID among HNC survivors. TRIAL REGISTRATION: ClinicalTrials.gov identifier NCT03831100 .

Mapping gene flow between ancient hominins through demography-aware inference of the ancestral recombination graph.

The sequencing of Neanderthal and Denisovan genomes has yielded many new insights about interbreeding events between extinct hominins and the ancestors of modern humans. While much attention has been paid to the relatively recent gene flow from Neanderthals and Denisovans into modern humans, other instances of introgression leave more subtle genomic evidence and have received less attention. Here, we present a major extension of the ARGweaver algorithm, called ARGweaver-D, which can infer local genetic relationships under a user-defined demographic model that includes population splits and migration events. This Bayesian algorithm probabilistically samples ancestral recombination graphs (ARGs) that specify not only tree topologies and branch lengths along the genome, but also indicate migrant lineages. The sampled ARGs can therefore be parsed to produce probabilities of introgression along the genome. We show that this method is well powered to detect the archaic migration into modern humans, even with only a few samples. We then show that the method can also detect introgressed regions stemming from older migration events, or from unsampled populations. We apply it to human, Neanderthal, and Denisovan genomes, looking for signatures of older proposed migration events, including ancient humans into Neanderthal, and unknown archaic hominins into Denisovans. We identify 3% of the Neanderthal genome that is putatively introgressed from ancient humans, and estimate that the gene flow occurred between 200-300kya. We find no convincing evidence that negative selection acted against these regions. Finally, we predict that 1% of the Denisovan genome was introgressed from an unsequenced, but highly diverged, archaic hominin ancestor. About 15% of these "super-archaic" regions-comprising at least about 4Mb-were, in turn, introgressed into modern humans and continue to exist in the genomes of people alive today.

Cross-Sectional Associations among Components of Injustice Appraisals and Functioning in Adolescents With Chronic Pain.

OBJECTIVE: Pain-related appraisals, including pain-related injustice, impact the development and maintenance of chronic pain. This cross-sectional study aimed to examine the relationship between the cognitive-emotional components of pain-related injustice-blame/unfairness and severity/irreparability of loss-and functioning in a mixed sample of adolescents with chronic pain. METHODS: Pediatric patients age 11-18 years (N = 408) completed forms assessing pain-related injustice, pain intensity, and physical and psychosocial functioning as part of their routine assessment in a pediatric chronic pain clinic between January 2014 and January 2019. A series of hierarchical regressions were used to evaluate the relationships among the separate components of pain-related injustice appraisals and functioning. RESULTS: Pain intensity and blame/unfairness appraisals were significantly associated with emotional functioning with blame/unfairness being the stronger association (ß = -.27). Blame/unfairness appraisals, severity/irreparability appraisals, and pain intensity were significantly associated with physical functioning with pain intensity being the strongest association (ß = .36). Pain intensity, blame/unfairness appraisals, and severity/irreparability appraisals were significantly associated with social functioning with blame/unfairness being the strongest association (ß = -.34). Pain intensity and severity/irreparability appraisals were significantly associated with school functioning with severity/irreparability being the stronger association (ß = -.19). CONCLUSIONS: These results lend further support to incorporating pain-related injustice appraisals in standard clinical pain assessments. Treatment practices should target the specific injustice appraisals and domains of functioning impacted for each pediatric patient with chronic pain.

Crossover interference and sex-specific genetic maps shape identical by descent sharing in close relatives.

Simulations of close relatives and identical by descent (IBD) segments are common in genetic studies, yet most past efforts have utilized sex averaged genetic maps and ignored crossover interference, thus omitting features known to affect the breakpoints of IBD segments. We developed Ped-sim, a method for simulating relatives that can utilize either sex-specific or sex averaged genetic maps and also either a model of crossover interference or the traditional Poisson model for inter-crossover distances. To characterize the impact of previously ignored mechanisms, we simulated data for all four combinations of these factors. We found that modeling crossover interference decreases the standard deviation of pairwise IBD proportions by 10.4% on average in full siblings through second cousins. By contrast, sex-specific maps increase this standard deviation by 4.2% on average, and also impact the number of segments relatives share. Most notably, using sex-specific maps, the number of segments half-siblings share is bimodal; and when combined with interference modeling, the probability that sixth cousins have non-zero IBD sharing ranges from 9.0 to 13.1%, depending on the sexes of the individuals through which they are related. We present new analytical results for the distributions of IBD segments under these models and show they match results from simulations. Finally, we compared IBD sharing rates between simulated and real relatives and find that the combination of sex-specific maps and interference modeling most accurately captures IBD rates in real data. Ped-sim is open source and available from https://github.com/williamslab/ped-sim.

Spinal cord stimulation for treatment of chronic neuropathic pain in adolescent patients: a single-institution series, systematic review, and individual participant data meta-analysis.

OBJECTIVE: Neuropathic pain is undertreated in children. Neurosurgical treatments of pediatric chronic pain are limited by the absence of both US Food and Drug Administration approval and pediatric-specific hardware, as well as weak referral patterns due to a lack of physician education. This study presents a single-institution retrospective case series of spinal cord stimulation (SCS) in children ≤ 19 years of age and a systematic review of SCS in children. The authors' findings may further validate the role of SCS as an effective treatment modality for varied neuropathic pain syndromes found in pediatric patients. METHODS: The study was a single-center, single-surgeon, retrospective case series of individuals treated between July 2017 and May 2022. The outcomes for pediatric patients with chronic neuropathic pain syndromes indicated by the multidisciplinary pain clinic for evaluation for SCS were cataloged. A systematic review and individual participant data (IPD) meta-analysis was performed for cases treated until May 2022, using PubMed, EMBASE, and Scopus to characterize outcomes of children with neuropathic pain treated with SCS. RESULTS: Twelve patients were evaluated and 9 were indicated for percutaneous or buried lead trials. Seven female and 2 male patients between the ages of 13 and 19 years were implanted with trial leads. Eight of 9 (89%) patients went on to receive permanent systems. The average trial length was 6 days, and the length of stay for both trial and implant was less than 1 day. Complication rates due to CSF leaks were 22% and 0% for trial and implant, respectively. Visual analog scale pain scores decreased from 9.2 to 2.9 (p = 0.0002) and the number of medications decreased from 4.9 to 2.1 (p = 0.0005). Functional status also improved for each patient. A systematic review identified 13 studies describing pediatric patients with SCS, including 12 providing IPD on 30 patients. In the IPD meta-analysis, pain was reduced in 16/16 (100%) of patients following surgery and in 25/26 (96.2%) at last follow-up. Medication use was decreased in 16/21 (76.2%), and functional outcomes were improved in 29/29 (100%). The complication rate was 5/30 (16.7%). CONCLUSIONS: SCS effectively decreases pain and medication use for pediatric neuropathic pain syndromes. Patients also report improved functional status, including improved matriculation, gainful employment, and physical activity. There is minimal high-quality literature describing neuromodulation for pain in children. Neuromodulation should be considered earlier as a viable alternative to escalating use of multiple drugs and as a potential mechanism to address tolerance, dependence, and addiction in pediatric patients.

Interprofessional Education: Current State in Psychology Training.

Healthcare reform has led to the consideration of interprofessional team-based, collaborative care as a way to provide comprehensive, high-quality care to patients and families. Interprofessional education is the mechanism by which the next generation health professional workforce is preparing for the future of health care-team-based, collaborative care. This literature review explored the extent and content of published studies documenting Interprofessional Education (IPE) activities with psychology trainees across learner level. A systematic review following PRISMA guidelines was conducted of studies describing IPE involving psychology learners. Electronic databases (MEDLINE, CINAHL, PsychINFO, and EMBASE) were searched for the following terms: inter/multi-professional education/practice, inter/multidisciplinary education/practice, and psychology/psychologists. Thirty-seven articles were identified that included psychology in clinical outcome studies or other reviews of interprofessional education initiatives. The review addresses the nature of current IPE learning activities, the impact of IPE activities on participating trainees, opportunities for, and challenges of, involving psychology trainees in IPE, and future directions for research. This review illuminates the relative paucity of the literature about IPE in psychology training. Given the trend toward increasing team-based collaborative care, the limited inclusion of psychology in the IPE literature is concerning. The next generation of health professional trainees is learning about, from, and with each other with the objective of building collaboration and teamwork. Given the few articles documenting psychology trainees' involvement in IPE, future health professionals quite possibly will have limited understanding of, and contact with, psychologists. Our findings are a call to action for greater psychology involvement in IPE.

Inferring Identical-by-Descent Sharing of Sample Ancestors Promotes High-Resolution Relative Detection.

As genetic datasets increase in size, the fraction of samples with one or more close relatives grows rapidly, resulting in sets of mutually related individuals. We present DRUID-deep relatedness utilizing identity by descent-a method that works by inferring the identical-by-descent (IBD) sharing profile of an ungenotyped ancestor of a set of close relatives. Using this IBD profile, DRUID infers relatedness between unobserved ancestors and more distant relatives, thereby combining information from multiple samples to remove one or more generations between the deep relationships to be identified. DRUID constructs sets of close relatives by detecting full siblings and also uses an approach to identify the aunts/uncles of two or more siblings, recovering 92.2% of real aunts/uncles with zero false positives. In real and simulated data, DRUID correctly infers up to 10.5% more relatives than PADRE when using data from two sets of distantly related siblings, and 10.7%-31.3% more relatives given two sets of siblings and their aunts/uncles. DRUID frequently infers relationships either correctly or within one degree of the truth, with PADRE classifying 43.3%-58.3% of tenth degree relatives in this way compared to 79.6%-96.7% using DRUID.

Evaluating the contribution of rare variants to type 2 diabetes and related traits using pedigrees.

A major challenge in evaluating the contribution of rare variants to complex disease is identifying enough copies of the rare alleles to permit informative statistical analysis. To investigate the contribution of rare variants to the risk of type 2 diabetes (T2D) and related traits, we performed deep whole-genome analysis of 1,034 members of 20 large Mexican-American families with high prevalence of T2D. If rare variants of large effect accounted for much of the diabetes risk in these families, our experiment was powered to detect association. Using gene expression data on 21,677 transcripts for 643 pedigree members, we identified evidence for large-effect rare-variant cis-expression quantitative trait loci that could not be detected in population studies, validating our approach. However, we did not identify any rare variants of large effect associated with T2D, or the related traits of fasting glucose and insulin, suggesting that large-effect rare variants account for only a modest fraction of the genetic risk of these traits in this sample of families. Reliable identification of large-effect rare variants will require larger samples of extended pedigrees or different study designs that further enrich for such variants.

Race, not socioeconomic disparities, correlates with survival in human papillomavirus-negative oropharyngeal cancer: A retrospective study.

PURPOSE: Investigate the impact of black versus white race, socioeconomic status (SES), and comorbidity burden on oropharyngeal cancer (OPC) survival. MATERIALS AND METHODS: This study retrospectively analyzed patients diagnosed between 1991 and 2012 at an urban tertiary care center with a high volume of head and neck cancer referrals. Data gathered included demographics, human papilloma virus (HPV) status, follow-up time, comorbidities, smoking history, and overall survival. SES was extrapolated from the 2000 and 2010 censuses. Analysis of variance, chi-square tests, multivariable Cox proportional hazards models, Cox proportional hazards regression, Kaplan Meier curves and the log-rank test were utilized. RESULTS: Of 208 charts reviewed, 192 patients met inclusion criteria. Black patients had significantly (p < 0.001) poorer survival at 1, 2, and 5 years than white patients (5-year survival: 32% vs 64%); this discrepancy persisted in only HPV-negative disease (20% vs 50%). In the HPV-negative subgroup, there was no racial difference in treatment modality received, Charlson Comorbidity Index, and proportion receiving inadequate, noncurative or no treatment. Univariate analysis identified significant differences in median household income, education level, and stage at presentation between black and white subgroups. Multivariate analysis identified white race and HPV-positive status as independent predictors of overall survival, but SES and stage at presentation were not. CONCLUSION: SES did not explain the greater survival in HPV-negative white versus black patients. This indicates that race is an independent predictor of survival; future studies should examine more accurate indicators of SES and genetic differences in tumors of black and white patients.

Does insurance type influence overall survival in patients with laryngeal squamous cell carcinoma?

OBJECTIVE: Patients with head and neck cancer with Medicaid or no insurance present at a more advanced stage and have lower survival. This study is one of the first to examine the relationship between specific insurance types and overall survival for laryngeal squamous cell carcinoma patients. STUDY DESIGN: Retrospective chart review. SETTING: Henry Ford Cancer Institute. SUBJECTS AND METHODS: A retrospective database review was performed using the Henry Ford Virtual Data Warehouse Tumor Registry. Six hundred and fifty patients diagnosed with laryngeal squamous cell carcinoma were identified. Insurance groups analyzed were fee for service, health maintenance organization, Henry Ford Medical Group - a managed care type insurance, Medicare and Medicaid/uninsured. Cox proportional hazards and Kaplan-Meier curves were generated to analyze overall survival and display survival differences respectively. RESULTS: The uninsured group had the lowest median survival time of 29.8 months (95% CI: 20.3-44.8) and the highest HR of 1.85 (95% CI 1.16-2.93) as compared to the HMO group at p < 0.001. Patients with fee for service insurance had longer overall survival compared to the other insurance types. Patients with fee for service insurance also had a high proportion of patients with advanced stage disease, but a younger mean age. Henry Ford Medical Group had a higher mean age and no statistically significant difference in survival when compared to fee for service. (p = 0.999) After controlling for socioeconomic status, insurance type remains a significant predictor of overall survival. CONCLUSIONS: Fee for service had the highest overall survival of the different insurance types, but it was only statistically significant when compared to the Medicaid/uninsured group.