Objective
To define the genetic landscape of amyotrophic lateral sclerosis (ALS) and assess the contribution of possible oligogenic inheritance, we aimed to comprehensively sequence 17 known ALS ...genes in 391 ALS patients from the United States.
Methods
Targeted pooled‐sample sequencing was used to identify variants in 17 ALS genes. Fragment size analysis was used to define ATXN2 and C9ORF72 expansion sizes. Genotype–phenotype correlations were made with individual variants and total burden of variants. Rare variant associations for risk of ALS were investigated at both the single variant and gene level.
Results
A total of 64.3% of familial and 27.8% of sporadic subjects carried potentially pathogenic novel or rare coding variants identified by sequencing or an expanded repeat in C9ORF72 or ATXN2; 3.8% of subjects had variants in >1 ALS gene, and these individuals had disease onset 10 years earlier (p = 0.0046) than subjects with variants in a single gene. The number of potentially pathogenic coding variants did not influence disease duration or site of onset.
Interpretation
Rare and potentially pathogenic variants in known ALS genes are present in >25% of apparently sporadic and 64% of familial patients, significantly higher than previous reports using less comprehensive sequencing approaches. A significant number of subjects carried variants in >1 gene, which influenced the age of symptom onset and supports oligogenic inheritance as relevant to disease pathogenesis. ANN NEUROL 2015;77:100–113
Expanded hexanucleotide repeats in the chromosome 9 open reading frame 72 (C9orf72) gene are the most common genetic cause of ALS and frontotemporal degeneration (FTD). Here, we identify nuclear RNA ...foci containing the hexanucleotide expansion (GGGGCC) in patient cells, including white blood cells, fibroblasts, glia, and multiple neuronal cell types (spinal motor, cortical, hippocampal, and cerebellar neurons). RNA foci are not present in sporadic ALS, familial ALS/FTD caused by other mutations (SOD1, TDP-43 , or tau), Parkinson disease, or nonneurological controls. Antisense oligonucleotides (ASOs) are identified that reduce GGGGCC-containing nuclear foci without altering overall C9orf72 RNA levels. By contrast, siRNAs fail to reduce nuclear RNA foci despite marked reduction in overall C9orf72 RNAs. Sustained ASO-mediated lowering of C9orf72 RNAs throughout the CNS of mice is demonstrated to be well tolerated, producing no behavioral or pathological features characteristic of ALS/FTD and only limited RNA expression alterations. Genome-wide RNA profiling identifies an RNA signature in fibroblasts from patients with C9orf72 expansion. ASOs targeting sense strand repeat-containing RNAs do not correct this signature, a failure that may be explained, at least in part, by discovery of abundant RNA foci with C9orf72 repeats transcribed in the antisense (GGCCCC) direction, which are not affected by sense strand-targeting ASOs. Taken together, these findings support a therapeutic approach by ASO administration to reduce hexanucleotide repeat-containing RNAs and raise the potential importance of targeting expanded RNAs transcribed in both directions.
Late onset Alzheimer's disease (LOAD) etiology is influenced by complex interactions between genetic and environmental risk factors. Large-scale genome wide association studies (GWAS) for LOAD have ...identified 10 novel risk genes: ABCA7, BIN1, CD2AP, CD33, CLU, CR1, EPHA1, MS4A6A, MS4A6E, and PICALM. We sought to measure the influence of GWAS single nucleotide polymorphisms (SNPs) and gene expression levels on clinical and pathological measures of AD in brain tissue from the parietal lobe of AD cases and age-matched, cognitively normal controls. We found that ABCA7, CD33, and CR1 expression levels were associated with clinical dementia rating (CDR), with higher expression being associated with more advanced cognitive decline. BIN1 expression levels were associated with disease progression, where higher expression was associated with a delayed age at onset. CD33, CLU, and CR1 expression levels were associated with disease status, where elevated expression levels were associated with AD. Additionally, MS4A6A expression levels were associated with Braak tangle and Braak plaque scores, with elevated expression levels being associated with more advanced brain pathology. We failed to detect an association between GWAS SNPs and gene expression levels in our brain series. The minor allele of rs3764650 in ABCA7 is associated with age at onset and disease duration, and the minor allele of rs670139 in MS4A6E was associated with Braak tangle and Braak plaque score. These findings suggest that expression of some GWAS genes, namely ABCA7, BIN1, CD33, CLU, CR1 and the MS4A family, are altered in AD brains.
Noncoding expansions of a hexanucleotide repeat (GGGGCC) in the C9orf72 gene are the most common cause of familial amyotrophic lateral sclerosis and frontotemporal dementia. Here we report transgenic ...mice carrying a bacterial artificial chromosome (BAC) containing the full human C9orf72 gene with either a normal allele (15 repeats) or disease-associated expansion (∼100–1,000 repeats; C9-BACexp). C9-BACexp mice displayed pathologic features seen in C9orf72 expansion patients, including widespread RNA foci and repeat-associated non-ATG (RAN) translated dipeptides, which were suppressed by antisense oligonucleotides targeting human C9orf72. Nucleolin distribution was altered, supporting that either C9orf72 transcripts or RAN dipeptides promote nucleolar dysfunction. Despite early and widespread production of RNA foci and RAN dipeptides in C9-BACexp mice, behavioral abnormalities and neurodegeneration were not observed even at advanced ages, supporting the hypothesis that RNA foci and RAN dipeptides occur presymptomatically and are not sufficient to drive neurodegeneration in mice at levels seen in patients.
•Transgenic mice expressing the C9orf72 repeat expansion were generated•C9-BACexp mice develop widespread RNA foci and RAN peptide pathology•Expanded C9orf72 led to altered nucleolin distribution•RNA foci and RAN peptides can be suppressed by ASOs to human C9orf72
Repeat expansions in C9orf72 are the most common cause of ALS and FTD. O’Rourke et al. generated BAC transgenic mice with expanded human C9orf72 that develop widespread RNA foci and DPR proteins, but lack neurodegeneration.
Context-dependent genetic effects, including genotype-by-environment and genotype-by-sex interactions, are a potential mechanism by which genetic variation of complex traits is maintained in ...populations. Pleiotropic genetic effects are also thought to play an important role in evolution, reflecting functional and developmental relationships among traits. We examine context-dependent genetic effects at pleiotropic loci associated with normal variation in multiple metabolic syndrome (MetS) components (obesity, dyslipidemia, and diabetes-related traits). MetS prevalence is increasing in Western societies and, while environmental in origin, presents substantial variation in individual response. We identify 23 pleiotropic MetS quantitative trait loci (QTL) in an F(16) advanced intercross between the LG/J and SM/J inbred mouse strains (Wustl:LG,SM-G16; n = 1002). Half of each family was fed a high-fat diet and half fed a low-fat diet; and additive, dominance, and parent-of-origin imprinting genotypic effects were examined in animals partitioned into sex, diet, and sex-by-diet cohorts. We examine the context-dependency of the underlying additive, dominance, and imprinting genetic effects of the traits associated with these pleiotropic QTL. Further, we examine sequence polymorphisms (SNPs) between LG/J and SM/J as well as differential expression of positional candidate genes in these regions. We show that genetic associations are different in different sex, diet, and sex-by-diet settings. We also show that over- or underdominance and ecological cross-over interactions for single phenotypes may not be common, however multidimensional synthetic phenotypes at loci with pleiotropic effects can produce situations that favor the maintenance of genetic variation in populations. Our findings have important implications for evolution and the notion of personalized medicine.
Abstract Study Objective Long-acting reversible contraceptive (LARC) methods can prevent teen pregnancy yet remain underutilized by adolescents in the United States. Pediatric providers are well ...positioned to discuss LARCs with adolescents, but little is known about how counseling should occur in pediatric primary care settings. We explored adolescent womens' attitudes and experiences with LARCs to inform the development of adolescent-centered LARC counseling strategies. Design Qualitative analysis of one-on-one interviews. Setting Participants were recruited from 2 urban school-based, primary care centers. Participants Thirty adolescent women aged 14-18 years, diverse in race/ethnicity, and sexual experience. Interventions Interviews were audio-recorded, transcribed, and coded using inductive and deductive coding. Main Outcome Measure Major themes were identified to integrate LARC-specific adolescent preferences into existing counseling approaches. Results Participants (mean age, 16.2 years; range, 14-18 years) represented a diverse range of racial and/or ethnic identities. Half (15/30) were sexually active and 17% (5/30) reported current or past LARC use. Five themes emerged regarding key factors that influence LARC choice, including: (1) strong preferences about device-specific characteristics; (2) previous exposure to information about LARCs from peers, family members, or health counseling sessions; (3) knowledge gaps about LARC methods that affect informed decision-making; (4) personal circumstances or experiences that motivate a desire for effective and/or long-acting contraception; and (5) environmental constraints and supports that might influence adolescent access to LARCs. Conclusion We identified 5 factors that influence LARC choice among adolescent women and propose a framework for incorporating these factors into contraceptive counseling services in pediatric primary care settings.
Abstract Purpose The purpose of this study was to describe the implementation of a program that provides long-acting reversible contraception (LARC) services within school-based health centers ...(SBHCs) and to identify barriers and facilitators to implementation as reported by SBHC clinicians and administrators, public health officials, and community partners. Methods We conducted 14 semistructured interviews with key informants involved in the implementation of LARC services. Key informants included SBHC clinicians and administrators, public health officials, and community partners. We used a content analysis approach to analyze interview transcripts for themes. We explored barriers to and facilitators of LARC service delivery across and within key informant groups. Results The most cited barriers across key informant groups were as follows: perceived lack of provider procedural skills and bias and negative attitudes about LARC methods. The most common facilitators identified across groups were as follows: clear communication strategies, contraceptive counseling practice changes, provider trainings, and stakeholder engagement. Two additional barriers emerged in specific key informant groups. Technical and logistical barriers to LARC service delivery were cited heavily by SBHC administrative staff, community partners, and public health officials. Expense and billing was a major barrier to SBHC administrative staff. Conclusions LARC counseling and procedural services can be implemented in an SBHC setting to promote access to effective contraceptive options for adolescent women.
Whole genome sequencing has opened the doors to Investigative genetic genealogy (IGG) analysis of challenging forensic samples that are not suitable for microarray genotyping. These samples still do ...not typically achieve high enough coverage for direct genotype calling, therefore a pipeline for imputation from low coverage sequencing data was evaluated using data from the 1000 Genomes Project. This pipeline generated results suitable for IGG down to 0.25X coverage. Additionally, forensic samples from a variety of tissue types and input amounts were sequenced and successfully uploaded to genetic genealogy databases after imputation.
PDF
