Abstract Objective: Charcot‐Marie‐Tooth (CMT) disease comprises a large number of genetically distinct forms of inherited peripheral neuropathies. The relative uniform phenotypes in many patients with CMT make it difficult to decide which of the over 35 known CMT genes are affected in a given patient. Genetic testing decision trees are therefore broadly based on a small number of major subtypes (eg, CMT1, CMT2) and the observed mutation frequency for CMT genes. Since conventional genetic testing is expensive many rare genes are not being tested for at all. Methods: Whole‐exome sequencing has recently been introduced as a novel and alternative approach. This method is capable of resequencing a nearly complete set of coding exons in an individual. We performed whole‐exome sequencing in an undiagnosed family with CMT. Results: Within over 24,000 variants detected in 2 exomes of a CMT family, we identified a nonsynonymous GJB1 ( Cx32 ) mutation. This variant had been reported previously as pathogenic in X‐linked CMT families. Sanger sequencing confirmed complete cosegregation in the family. Affected individuals had a marked early involvement of the upper distal extremities and displayed a mild reduction of nerve conduction velocities. Interpretation: We have shown for the first time in a genetically highly heterogeneous dominant disease that exome sequencing is a valuable method for comprehensive medical diagnosis. Further improvements of exon capture design, next‐generation sequencing accuracy, and a constant price decline will soon lead to the adoption of genomic approaches in gene testing of Mendelian disease. Ann Neurol 2011;
The Alzheimer's Disease Sequencing Project (ADSP) is an initiative to identify rare genetic variation influencing Late Onset Alzheimer's Disease (LOAD) risk. As part of the ADSP, we performed whole-genome sequencing (WGS) in 67 Caribbean Hispanic (CH) and 44 non-Hispanic white (NHW) extended families multiply affected by LOAD, followed by extensive quality control, variant filtering, and gene-based association tests. WGS data were generated for 351 subjects from 67 CH families and 197 subjects from 44 NHW families, including both AD and cognitively intact relatives. Alignment was performed using the Burrows-Wheeler algorithm, followed by genotype calling using a consensus calling pipeline that used both GATK genotype calls and ATLAS genotype calls. Variants were annotated for allele frequency and predicted functional impact, categorized into damaging (e.g., loss of function, high CADD scores, etc) and likely damaging (e.g., non-synonymous, moderate CADD, etc). We performed gene-based association testing, accounting for family structure using the FSKAT software. Association was performed using rare variants (MAF<0.01) and two models (damaging set only; damaging and likely damaging), with CH and NHW sets analyzed separately. Examination of the 30 known LOAD genes (largely identified by GWAS-based meta-analyses) confirmed the role of rare functional variation in a number of genes, including CR1 (p =0.040 in NHW, p=0.049 in CH; damaging variants only) and SLC24A4 (p=0.002 in NHW, p=0.040 in CH). Other candidate genes showed nominal association in one but not both datasets (AKAP9, FERMT2, GRN, HLA-DRB5, MEF2C in NHW dataset; BIN1, PTK2B in CH). Additional genes showed strong association in the CH dataset, with nominal association in the NHW. These include ATG2A (p=0.0003 in CH, p=0.02 in NHW), a gene involved in both autophagy and lipid droplet formation, and CD69 (p=0.00054 in CH, p=0.02 in NHW), a gene involved in cell proliferation. These results suggest rare, functional variation may influence LOAD risk in multiplex families, even among genes identified through common variation. We also show association with novel genes, ATG2A and CD69, with support from both CH and NHW families. Variants are currently being validated using other technologies, and follow-up and replication analyses are ongoing.
Abstract Cerebral amyloid angiopathy commonly co-occurs with amyloid β plaques and neurofibrillary degeneration and is proposed to contribute to cognitive impairment. However, the interplay among these pathologic changes of Alzheimer disease is not well understood. Here we replicate and extend findings of a recent study that suggested the association of cerebral amyloid angiopathy and cognitive impairment is mediated by neurofibrillary degeneration. We employed similar approaches but in a larger, clinical-based (as opposed to community-based) set of 4915 autopsied National Alzheimer’s Coordinating Center participants (60% with dementia). Neuropathologic lesions were measured ordinally; longitudinal change in cognition was used to measure cognitive impairment. Statistical analyses included ordinal logistic regression, mediation analyses and extension of models to include presence of APOE e4. We show a statistical interaction between cerebral amyloid angiopathy and neuritic plaques that impacts the burden of neurofibrillary tangles. Mediation analyses show that cerebral amyloid angiopathy is associated with cognitive impairment, but only by modifying the impact of neurofibrillary tangles on cognition. We expanded the mediation analysis to include APOE e4 and show similar results. Findings indicate that cerebral amyloid angiopathy plays an important role in the burden and impact of neurofibrillary degeneration contributing to cognitive impairment.
Background Alzheimer's disease is a common debilitating dementia with known heritability, for which 20 late onset susceptibility loci have been identified, but more remain to be discovered. This study sought to identify new susceptibility genes, using an alternative gene-wide analytical approach which tests for patterns of association within genes, in the powerful genome-wide association dataset of the International Genomics of Alzheimer's Project Consortium, comprising over 7 m genotypes from 25,580 Alzheimer's cases and 48,466 controls. Principal Findings In addition to earlier reported genes, we detected genome-wide significant loci on chromosomes 8 (TP53INP1, p = 1.4×10−6) and 14 (IGHV1-67 p = 7.9×10−8) which indexed novel susceptibility loci. Significance The additional genes identified in this study, have an array of functions previously implicated in Alzheimer's disease, including aspects of energy metabolism, protein degradation and the immune system and add further weight to these pathways as potential therapeutic targets in Alzheimer's disease.
Abstract Background Puerto Ricans, the second largest US Latino group, are underrepresented in genomic studies of Alzheimer disease (AD). We describe a multi‐source ascertainment approach, networking with community and governmental stakeholders, as part of the Puerto Rico (PR) Alzheimer Disease Initiative (PRADI) whose goal is to increase recruitment and retention of PR individuals in genomic research.The National Alzheimer’s disease Action Plan 2015‐2025 served as a framework for PRADI group that aims to fill two of the goals of the plan: increase research and education. Method We developed collaborative relationships with community and governmental organizations that serve the elderly and AD patients from 37/78 (47%) municipalities of PR to identify potential research participants. Trust and transparency were central to our interactions with community groups. We educated patients and caregivers about AD and their possible contribution to science. Bringing academia to the community encouraged participation. Additionally, we established relationships with multiple neurologists across PR caring for AD patients and their families. For recruitment and enrollment PRADI team members visited families in the homes, daycare facilities and clinics. All participants were assigned diagnoses by a clinical adjudication committee comprised of neurologists and neuropsychologists with expertise in AD and related dementias (ADRD) Result Since 2016 we have enrolled 1, 281 individuals. Among these 752 are unrelated individuals (193 AD, 170 mild cognitive impairment (MCI), 306 cognitively unimpaired (CU) and 83 with other diagnoses (OD). 529 individuals (195 AD, 76 MCI, 178 CU and 80 OD) were part of 155 multiplex AD families. Most families are from Eastern and Northern PR regions, reflecting dense population areas with large cities. Longitudinal follow‐up of the first 167 participants for diagnostic updates is complete. 64 individuals were ascertained in the continental US (cUS). Of the 167 individuals in the longitudinal follow‐up (3‐5 years), 7.2% progressed from either CU to MCI or AD, or MCI to AD. Conclusion The PRADI group multisource ascertainment approach enabled recruitment and retention of participants both in PR and the cUS. Longitudinal clinical data across the cohort further enriches the impact of genomic studies in a diverse population.
Abstract Background With over 5.1 million individuals, the Puerto Rican population makes up over 1.5% of the US population and is the 2nd largest Hispanic/Latino population in the continental US. There are an estimated of 60,000 cases of AD on the island. The Puerto Rico Alzheimer's and Related Dementias Initiatives (PRADI) cohort will both leverage and complement existing AD Resources, the Alzheimer Disease Sequencing Project (ADSP) with the inclusion of a diverse and underrepresented population. At present, the cohort consists of a total of 935 total participants including individuals from 115 multiplex AD families. There are 418 cases of dementia, 217 mild cognitive impairment, and 300 unrelated and family‐based controls. Method We examined the most successful strategy to recruit cases and controls as well as multiplex families for both case/control and family‐based genetic studies. We began by engaging a wide range of stakeholders across the island. The core activities of our team include relationship building, partnership development and maintenance, and coalition building. For the community outreach, we utilize mass media like newspapers, radio interviews, and focal group presentations and engaged the following stakeholder groups: Alzheimer disease day care centers, elderly housing in San Juan, senior day care centers, non‐profit organizations, private neurology offices, and other community‐based organizations such as the Alzheimer’s Association. Result The percent of patients recruited through each stakeholder group were 45.76% (428/935) from community outreach, 34.33% (321/935) from private neurologist practices, 18.93% (177/935) from senior day care centers and 0.96% (9/935) from Alzheimer disease day care centers. The mean age and standard deviation of cases and controls were 78.22 years (±9.37) and 70.84 years (±7.92) respectively. Examining the data with respect to multiplex family structure, we found that 53.77% of the families (including the largest families) came from private physician referral. Conclusion Partnering with diverse stakeholders and building coalitions proved to be effective as an outreach method for recruitment. Private physicians remain an excellent source for the identification of multiplex AD families for family‐based genetics study. Outreach community‐based approaches are highly successful mechanisms to educate and engage participants in genetic research.
The Alzheimer's Disease Sequencing Project (ADSP) undertook whole exome sequencing in 5,740 late-onset Alzheimer disease (AD) cases and 5,096 cognitively normal controls primarily of European ancestry (EA), among whom 218 cases and 177 controls were Caribbean Hispanic (CH). An age-, sex- and APOE based risk score and family history were used to select cases most likely to harbor novel AD risk variants and controls least likely to develop AD by age 85 years. We tested ~1.5 million single nucleotide variants (SNVs) and 50,000 insertion-deletion polymorphisms (indels) for association to AD, using multiple models considering individual variants as well as gene-based tests aggregating rare, predicted functional, and loss of function variants. Sixteen single variants and 19 genes that met criteria for significant or suggestive associations after multiple-testing correction were evaluated for replication in four independent samples; three with whole exome sequencing (2,778 cases, 7,262 controls) and one with genome-wide genotyping imputed to the Haplotype Reference Consortium panel (9,343 cases, 11,527 controls). The top findings in the discovery sample were also followed-up in the ADSP whole-genome sequenced family-based dataset (197 members of 42 EA families and 501 members of 157 CH families). We identified novel and predicted functional genetic variants in genes previously associated with AD. We also detected associations in three novel genes: IGHG3 (p = 9.8 × 10
Abstract Background The COVID‐19 pandemic has placed a demand on researchers to limit in‐person contact with participants, greatly impacting Alzheimer Disease (AD) research. To address this problem, we describe here an approach to using digital technology to continue nationwide clinical recruitment and ascertainment of biological samples while adhering to COVID‐19 guidelines and travel restrictions. Method To accomplish this, we considered a videoconferencing approach for remote delivery of cognitive assessments. A multi‐site panel of neurologists and clinical psychologists and a detailed literature review ensured a protocol that captures the best‐practices for administering assessments through videoconferencing while ensuring consistency between remote and in‐person administration. Clinical coordinators underwent training to ensure good agreement with in‐person administration. Most aspects of the cognitive assessments easily transferred to videoconferencing, though Trail Making A and B, and Digit Symbol‐Coding were removed to protect the integrity of the evaluation. Additionally, we coordinated the collection of biological samples with a national company, Quest Diagnostics, to provide phlebotomy services at the participant’s residence. All protocols were developed under the guidance of the Human Subjects Research Office at the University of Miami and with approval of local IRB. Result Our clinical coordinators completed over two dozen remote assessments using these protocols. Both cases and controls were enrolled, across various ethnic populations within our study. The distributions of age and 3MS were similar between in‐person and remote assessments. The uptake of videoconferencing enrollment varied among the age groups, level of impairment, at‐home support system and telemedicine readiness. For example, earlier‐onset groups had the best uptake, while older‐onset groups showed the least uptake due to a higher prevalence of telemedicine unreadiness (Lam et al., 2020; Bossen et al.,2015). Conclusion This study demonstrates that remote enrollment and ascertainment of biological samples through videoconferencing and partnering with national mobile phlebotomy services is feasible. This approach allows researchers to continue ascertainment efforts while maintaining their participants’ autonomy through informed consent and privacy throughout the process and minimizing their exposure to COVID‐19.
Abstract Background Amyloidosis in Alzheimer’s disease (AD) is a common feature that can be measured via cerebrospinal fluid (CSF), positron emission tomography (PET), and autopsy measures of neuritic plaques. While individual genome‐wide association studies (GWAS) have identified more than 40 loci as potential biological drivers of AD, fewer drivers of amyloidosis have been identified due to the small sample sizes in endophenotype analyses. Combining unimodal measures of amyloid into a larger multi‐modal analysis could provide new insight into mechanisms driving amyloidosis. The goal of this study was to conduct a large meta‐analysis of CSF‐, PET‐, and pathology‐derived metrics of amyloid positivity. Method 11,941 non‐Hispanic white participants (CSF = 2505, PET = 3976, Autopsy = 5460) from 14 cohorts were analyzed. To facilitate cross‐modality harmonization, a binarized amyloid status (negative/positive) was determined on an individual cohort basis using two approaches: a Gaussian mixture model clustering algorithm for CSF/PET measurements and CERAD thresholds (CERAD>sparse or CERAD ≤ sparse) for autopsy measures of amyloid pathology. In total, our analysis included 5,634 amyloid‐negative and 6,307 amyloid‐positive individuals. GWAS using a logistic regression model covarying for age and sex were performed in each of the 14 cohorts, and a meta‐analysis was performed within each modality. These meta‐analyses were followed with a multi‐modal meta‐analysis. The standard genome‐wide threshold of statistical significance (p < 5 × 10 −8 ) was applied. Additionally, we performed candidate analysis for the 39 previously published clinical AD or amyloid risk loci. Result Aside from variants within the APOE region, our multi‐modal meta‐analysis did not identify any genome‐wide loci (Figure 1). A lack of convergent GWAS signals was also observed when stratifying by age, sex, and APOE carrier status. However, our candidate gene analysis demonstrated some consistency across modalities. Two prior loci were significant in 2/3 modalities, including ABCA7 (rs4147929; p = 1.98 × 10 −4 ) and CLU (rs4236671; p = 0.001). Conclusion In the largest GWAS of brain amyloidosis, we found a lack of convergence across modalities, suggesting substantial heterogeneity across measures and cohorts. Candidate analyses highlight some consistent signals in ABCA7 and CLU . Results suggest continued emphasis on increasing sample sizes for endophenotype analyses and on standardized methodologies to reduce sample heterogeneity to improve statistical power.
