Complement factor H shows very strong association with Age-related Macular Degeneration (AMD), and recent data suggest that multiple causal variants are associated with disease. To refine the location of the disease associated variants, we characterized in detail the structural variation at CFH and its paralogs, including two copy number polymorphisms (CNP), CNP147 and CNP148, and several rare deletions and duplications. Examination of 34 AMD-enriched extended families (N = 293) and AMD cases (White N = 4210 Indian = 134; Malay = 140) and controls (White N = 3229; Indian = 117; Malay = 2390) demonstrated that deletion CNP148 was protective against AMD, independent of SNPs at CFH. Regression analysis of seven common haplotypes showed three haplotypes, H1, H6 and H7, as conferring risk for AMD development. Being the most common haplotype H1 confers the greatest risk by increasing the odds of AMD by 2.75-fold (95% CI = [2.51, 3.01]; p = 8.31×10−109); Caucasian (H6) and Indian-specific (H7) recombinant haplotypes increase the odds of AMD by 1.85-fold (p = 3.52×10−9) and by 15.57-fold (P = 0.007), respectively. We identified a 32-kb region downstream of Y402H (rs1061170), shared by all three risk haplotypes, suggesting that this region may be critical for AMD development. Further analysis showed that two SNPs within the 32 kb block, rs1329428 and rs203687, optimally explain disease association. rs1329428 resides in 20 kb unique sequence block, but rs203687 resides in a 12 kb block that is 89% similar to a noncoding region contained in ΔCNP148. We conclude that causal variation in this region potentially encompasses both regulatory effects at single markers and copy number.

Tuberculosis (TB) is a major public health burden worldwide, and more effective treatment is sorely needed. Consequently, uncovering causes of resistance to Mycobacterium tuberculosis (Mtb) infection is of special importance for vaccine design. Resistance to Mtb infection can be defined by a persistently negative tuberculin skin test (PTST-) despite living in close and sustained exposure to an active TB case. While susceptibility to Mtb is, in part, genetically determined, relatively little work has been done to uncover genetic factors underlying resistance to Mtb infection. We examined a region on chromosome 2q previously implicated in our genomewide linkage scan by a targeted, high-density association scan for genetic variants enhancing PTST- in two independent Ugandan TB household cohorts (n = 747 and 471). We found association with SNPs in neighboring genes ZEB2 and GTDC1 (peak meta p = 1.9 × 10) supported by both samples. Bioinformatic analysis suggests these variants may affect PTST- by regulating the histone deacetylase (HDAC) pathway, supporting previous results from transcriptomic analyses. An apparent protective effect of PTST- against body-mass wasting suggests a link between resistance to Mtb infection and healthy body composition. Our results provide insight into how humans may escape latent Mtb infection despite heavy exposure.

Objectives Speech sound disorder (SSD) is one of the most common communication disorders, with prevalence rates of 16% at 3 years of age, and an estimated 3.8% of children still presenting speech difficulties at 6 years of age. Several studies have identified promising associations between communication disorders and genes in brain and neuronal pathways, but there have been few studies focusing on SSD and its associated endophenotypes. Based on the hypothesis that neuronal genes may influence endophenotypes common to communication disorders, we focused on three genes related to brain and central nervous system functioning: dopamine D2 receptor (DRD2), arginine-vassopressin receptor 1a (AVPR1A), and microcephaly gene ASPM. Methods We examined the association of these genes with key endophenotypes of SSD – phonological memory measured by multisyllabic and nonword repetition, vocabulary measured by Expressive One Word Picture Vocabulary Test (EOWPVT) and Peabody Picture Vocabulary Test (PPVT), and reading decoding measured by Woodcock Reading Mastery Tests Revised – as well as the clinical phenotype of SSD. We genotyped tag SNPs in these genes and examined 498 individuals from 180 families. Results These data show several SNPs in all three genes were associated with phonological memory, vocabulary, and reading decoding with p<0.05. Notably, associations in AVPR1A (rs11832266) were significant after multiple testing correction. Gene-level tests showed DRD2 was associated with vocabulary, ASPM with vocabulary and reading decoding, and AVPR1A with all three endophenotypes. Conclusions Endophenotypes common to SSD, language impairment, and reading disability are all associated with these neuronal pathway genes.

Abstract. Interferon-γ (IFN-γ) is a key cytokine in the immune response to Mycobacterium tuberculosis (Mtb). Many studies established IFN-γ responses are influenced by host genetics, however differed widely by the study design and heritability estimation method. We estimated heritability of IFN-γ responses to Mtb culture filtrate (CF), ESAT-6, and Antigen 85B (Ag85B) in 1,104 Ugandans from a household contact study. Our method separately evaluates shared environmental and genetic variance, therefore heritability estimates were not upwardly biased, ranging from 11.6% for Ag85B to 22.9% for CF. Subset analyses of individuals with latent Mtb infection or without human immunodeficiency virus infection yielded higher heritability estimates, suggesting 10-30% of variation in IFN-γ is caused by a shared environment. Immunosuppression does not negate the role of genetics on IFN-γ response. These estimates are remarkably close to those reported for components of the innate immune response. These findings have implications for the interpretation of IFN-γ response assays and vaccine studies.

A predictive joint shared parameter model is proposed for discrete time-to-event and longitudinal data. A discrete survival model with frailty and a generalized linear mixed model for the longitudinal data are joined to predict the probability of events. This joint model focuses on predicting discrete time-to-event outcome, taking advantage of repeated measurements. We show that the probability of an event in a time window can be more precisely predicted by incorporating the longitudinal measurements. The model was investigated by comparison with a two-step model and a discrete time survival model. Results from both a study on the occurrence of tuberculosis and simulated data show that the joint model is superior to the other models in discrimination ability, especially as the latent variables related to both survival times and the longitudinal measurements depart from 0.