Citations

ABSTRACTRare variants have recently garnered an immense amount of attention in genetic association analysis. However, unlike methods traditionally used for single marker analysis in GWAS, rare variant analysis often requires some method of aggregation, since single marker approaches are poorly powered for typical sequencing study sample sizes. Advancements in sequencing technologies have rendered next‐generation sequencing platforms a realistic alternative to traditional genotyping arrays. Exome sequencing in particular not only provides base‐level resolution of genetic coding regions, but also a natural paradigm for aggregation via genes and exons. Here, we propose the use of penalized regression in combination with variant aggregation measures to identify rare variant enrichment in exome sequencing data. In contrast to marginal gene‐level testing, we simultaneously evaluate the effects of rare variants in multiple genes, focusing on gene‐based least absolute shrinkage and selection operator (LASSO) and exon‐based sparse group LASSO models. By using gene membership as a grouping variable, the sparse group LASSO can be used as a gene‐centric analysis of rare variants while also providing a penalized approach toward identifying specific regions of interest. We apply extensive simulations to evaluate the performance of these approaches with respect to specificity and sensitivity, comparing these results to multiple competing marginal testing methods. Finally, we discuss our findings and outline future research.

Objective To evaluate the horizontal and vertical stability of the quadrangular Le Fort I in patients with congenital cleft lip and palate. Design Prospective longitudinal study. Patients A total of 15 congenital cleft lip and palate patients treated with the maxillary quadrangular Le Fort I were enrolled. Intervention Lateral cephalometric radiographic examinations were obtained preoperatively, early postoperatively, and late postoperatively for four dental and skeletal landmarks. A questionnaire regarding patients' satisfaction with treatment and functional/cosmetic outcomes (airway, speech, mastication) was administered. Main Outcome Measures Surgical horizontal and vertical movement, late postsurgical horizontal and vertical movement, and surgical and postsurgical movement in relation to age and cleft type were evaluated using Spearman correlation coefficients, Wilcoxon signed rank tests, and Mann-Whitney tests. Results Surgical horizontal movements of all measured points showed significant changes. Significant differences of postsurgical horizontal movement were observed in younger patients versus adult patients. Significant differences of postsurgical horizontal movement were observed in unilateral cleft patients versus bilateral cleft patients. A high percentage of patients showed significant functional improvement in nasal airflow, speech, mastication, temporomandibular joint function, and mouth versus nose breathing. Conclusions The quadrangular Le Fort I is a functionally stable and a surgically predictable procedure for cleft lip and palate patients who present with midface deficiency. Patients under the age of 18 at the time of the osteotomy had a higher relapse rate than patients over 18 years of age. Younger patients who need surgery should be advised regarding the increased risk of skeletal relapse. Patients' satisfaction was high in all aesthetic- and function-related items on the questionnaire.

BACKGROUND The majority of patients diagnosed with clear cell renal cell carcinoma (ccRCC) have low‐risk disease with a < 10% chance of ccRCC‐specific death. DNA sequencing revealed that mutations in BAP1 (BRCA1 associated protein‐1) occur in 5% to 15% of ccRCC cases and are associated with poor outcomes. The vast majority of BAP1 mutations abolish protein expression. In this study, we used a highly sensitive and specific immunohistochemistry (IHC) assay to test whether BAP1 expression is an independent marker of ccRCC‐specific survival, particularly in patients with low‐risk disease. METHODS BAP1 expression was assessed, using IHC, in 1479 patients who underwent nephrectomy to treat clinically localized ccRCC. A centralized pathologist dichotomized patients as either BAP1‐positive or BAP1‐negative. The authors employed Kaplan‐Meier and Cox regression models to associate BAP1 expression with cancer‐specific survival. RESULTS A total of 10.5% of tumors were BAP1‐negative, 84.8% of tumors were BAP1‐positive, and 4.6% of tumors had ambiguous staining for BAP1. Patients with BAP1‐negative tumors have an increased risk of ccRCC‐related death (hazard ratio [HR] = 3.06; 95% confidence interval [CI] = 2.28‐4.10; P = 6.77 × 10 −14 ). BAP1 expression remained an independent marker of prognosis after adjusting for the UCLA integrated staging system (UISS) (HR = 1.67; 95% CI = 1.24‐2.25; P < .001). Finally, BAP1 was an independent prognostic marker in low‐risk patients with a Mayo Clinic stage, size, grade, and necrosis (SSIGN) score of ≤ 3 (HR = 3.24; 95% CI = 1.26‐8.33; P = .015). CONCLUSIONS This study used a large patient cohort to demonstrate that BAP1 expression is an independent marker of prognosis in patients with low‐risk (SSIGN≤ 3) ccRCC. Cancer 2014;1059–1067 . © 2014 American Cancer Society .

AbstractBackgroundMortality rates in patients with bullous pemphigoid (BP) are higher than those in age‐matched counterparts. However, the specific causes of death in BP subjects have not been evaluated systematically.ObjectivesWe sought to characterize the causes of death in patients with BP as recorded by death certificate and to compare these with death data for age‐ and location‐matched control subjects.MethodsThis was a retrospective cohort analysis conducted in a large tertiary referral center. Twenty‐seven participants who had a confirmed antemortem diagnosis of BP, were residents of Olmsted County, Minnesota, and had died between January 1, 1999, and January 1, 2009, were included in the study. Underlying cause of death and multiple causes of death data for the study population were compared with data sourced from the Centers for Disease Control and Prevention (CDC) for a control group matched by age and geographic location of origin by International Classification of Diseases, 10th Revision (ICD‐10) block, and specific ICD‐10 codes.ResultsComparisons of specific ICD‐10 codes revealed increased rates of sepsis (P = 0.031), dementia (P = 0.049), and major depressive disorder (P = 0.005) in the study group. The collective incidence of ICD‐10 codes for infections indicated that infections were more frequent contributors to death in the study group (P = 0.035).ConclusionsClinicians should be mindful of contributors to death in patients with BP and might consider screening for mental health issues, educating patients on the early symptoms of sepsis, and minimizing risk factors for infection.

AbstractPrurigo pigmentosa (PP) is a rare inflammatory dermatosis of unknown cause characterized by a predominantly truncal eruption of pruritic erythematous papules in a reticular pattern, resolving with hyperpigmentation. PP is twice as common in girls and women, and the mean age at onset is 25 years. Diagnosis of PP is challenging and is aided by characteristic histopathologic findings. We report a case of PP in a 17‐year‐old white boy. The eruption arose during strict adherence to a ketogenic diet.

ABSTRACTThe bone marrow provides a protective environment for acute myeloid leukemia (AML) cells that often allows leukemic stem cells to survive standard chemotherapeutic regimens. Targeting these leukemic stem cells within the bone marrow is critical for preventing relapse. We recently demonstrated that SDF‐1, a chemokine abundant in the bone marrow, induces apoptosis in AML cell lines and in patient samples expressing high levels of its receptor, CXCR4. Here we show that a subset of osteoblast lineage cells within the bone marrow can protect AML cells from undergoing apoptosis in response to the SDF‐1 naturally present in that location. In co‐culture systems, osteoblasts at various stages of differentiation protected AML cell lines and patient isolates from SDF‐1‐induced apoptosis. The differentiation of the osteoblast cell lines, MC3T3 and W‐20‐17, mediated this protection via a cell contact‐independent mechanism. In contrast, bone marrow‐derived mesenchymal cells, the precursors of osteoblasts, induced apoptosis in AML cells via a CXCR4‐dependent mechanism and failed to protect AML cells from exogenously added SDF‐1. These results indicate that osteoblasts in the process of differentiation potently inhibit the SDF‐1‐driven apoptotic pathway of CXCR4‐expressing AML cells residing in the bone marrow. Drugs targeting this protective mechanism could potentially provide a new approach to treating AML by enhancing the SDF‐1‐induced apoptosis of AML cells residing within the bone marrow microenvironment. J. Cell. Biochem. 115: 1128–1137, 2014. © 2013 Wiley Periodicals, Inc.