Indigenous Australian genomes show deep structure and rich novel variation.

The Indigenous peoples of Australia have a rich linguistic and cultural history. How this relates to genetic diversity remains largely unknown because of their limited engagement with genomic studies. Here we analyse the genomes of 159 individuals from four remote Indigenous communities, including people who speak a language (Tiwi) not from the most widespread family (Pama-Nyungan). This large collection of Indigenous Australian genomes was made possible by careful community engagement and consultation. We observe exceptionally strong population structure across Australia, driven by divergence times between communities of 26,000-35,000 years ago and long-term low but stable effective population sizes. This demographic history, including early divergence from Papua New Guinean (47,000 years ago) and Eurasian groups1, has generated the highest proportion of previously undescribed genetic variation seen outside Africa and the most extended homozygosity compared with global samples. A substantial proportion of this variation is not observed in global reference panels or clinical datasets, and variation with predicted functional consequence is more likely to be homozygous than in other populations, with consequent implications for medical genomics2. Our results show that Indigenous Australians are not a single homogeneous genetic group and their genetic relationship with the peoples of New Guinea is not uniform. These patterns imply that the full breadth of Indigenous Australian genetic diversity remains uncharacterized, potentially limiting genomic medicine and equitable healthcare for Indigenous Australians.

The landscape of genomic structural variation in Indigenous Australians.

Indigenous Australians harbour rich and unique genomic diversity. However, Aboriginal and Torres Strait Islander ancestries are historically under-represented in genomics research and almost completely missing from reference datasets1-3. Addressing this representation gap is critical, both to advance our understanding of global human genomic diversity and as a prerequisite for ensuring equitable outcomes in genomic medicine. Here we apply population-scale whole-genome long-read sequencing4 to profile genomic structural variation across four remote Indigenous communities. We uncover an abundance of large insertion-deletion variants (20-49 bp; n = 136,797), structural variants (50 b-50 kb; n = 159,912) and regions of variable copy number (>50 kb; n = 156). The majority of variants are composed of tandem repeat or interspersed mobile element sequences (up to 90%) and have not been previously annotated (up to 62%). A large fraction of structural variants appear to be exclusive to Indigenous Australians (12% lower-bound estimate) and most of these are found in only a single community, underscoring the need for broad and deep sampling to achieve a comprehensive catalogue of genomic structural variation across the Australian continent. Finally, we explore short tandem repeats throughout the genome to characterize allelic diversity at 50 known disease loci5, uncover hundreds of novel repeat expansion sites within protein-coding genes, and identify unique patterns of diversity and constraint among short tandem repeat sequences. Our study sheds new light on the dimensions and dynamics of genomic structural variation within and beyond Australia.

Equitable Expanded Carrier Screening Needs Indigenous Clinical and Population Genomic Data.

Expanded carrier screening (ECS) for recessive monogenic diseases requires prior knowledge of genomic variation, including DNA variants that cause disease. The composition of pathogenic variants differs greatly among human populations, but historically, research about monogenic diseases has focused mainly on people with European ancestry. By comparison, less is known about pathogenic DNA variants in people from other parts of the world. Consequently, inclusion of currently underrepresented Indigenous and other minority population groups in genomic research is essential to enable equitable outcomes in ECS and other areas of genomic medicine. Here, we discuss this issue in relation to the implementation of ECS in Australia, which is currently being evaluated as part of the national Government's Genomics Health Futures Mission. We argue that significant effort is required to build an evidence base and genomic reference data so that ECS can bring significant clinical benefit for many Aboriginal and/or Torres Strait Islander Australians. These efforts are essential steps to achieving the Australian Government's objectives and its commitment "to leveraging the benefits of genomics in the health system for all Australians." They require culturally safe, community-led research and community involvement embedded within national health and medical genomics programs to ensure that new knowledge is integrated into medicine and health services in ways that address the specific and articulated cultural and health needs of Indigenous people. Until this occurs, people who do not have European ancestry are at risk of being, in relative terms, further disadvantaged.

A globally diverse reference alignment and panel for imputation of mitochondrial DNA variants.

BACKGROUND: Variation in mitochondrial DNA (mtDNA) identified by genotyping microarrays or by sequencing only the hypervariable regions of the genome may be insufficient to reliably assign mitochondrial genomes to phylogenetic lineages or haplogroups. This lack of resolution can limit functional and clinical interpretation of a substantial body of existing mtDNA data. To address this limitation, we developed and evaluated a large, curated reference alignment of complete mtDNA sequences as part of a pipeline for imputing missing mtDNA single nucleotide variants (mtSNVs). We call our reference alignment and pipeline MitoImpute. RESULTS: We aligned the sequences of 36,960 complete human mitochondrial genomes downloaded from GenBank, filtered and controlled for quality. These sequences were reformatted for use in imputation software, IMPUTE2. We assessed the imputation accuracy of MitoImpute by measuring haplogroup and genotype concordance in data from the 1000 Genomes Project and the Alzheimer's Disease Neuroimaging Initiative (ADNI). The mean improvement of haplogroup assignment in the 1000 Genomes samples was 42.7% (Matthew's correlation coefficient = 0.64). In the ADNI cohort, we imputed missing single nucleotide variants. CONCLUSION: These results show that our reference alignment and panel can be used to impute missing mtSNVs in existing data obtained from using microarrays, thereby broadening the scope of functional and clinical investigation of mtDNA. This improvement may be particularly useful in studies where participants have been recruited over time and mtDNA data obtained using different methods, enabling better integration of early data collected using less accurate methods with more recent sequence data.

Beyond platitudes: a qualitative study of Australian Aboriginal people's perspectives on biobanking.

BACKGROUND: Biobanks are vital resources for genetics and genomics, and it is broadly recognised that for maximal benefit it is essential that they include samples and data from diverse ancestral groups. The inclusion of First Nations people, in particular, is important to prevent biobanking research from exacerbating existing health inequities, and to ensure that these communities share in the benefits arising from research. AIMS: To explore the perspectives of Australian Aboriginal people whose tissue - or that of their family members - has been stored in the biobank of the National Centre for Indigenous Genomics (NCIG). METHODS: Semi-structured interviews with 42 Aboriginal people from the Titjikala, Galiwinku, Tiwi Islands, Yarrabah, Fitzroy Crossing, Derby, One Arm Point and Mulan communities, as well as a formal discussion with A. Hermes, an Indigenous Community Engagement Coordinator at the NCIG who had conducted the interviews. The interviews and the structured discussion were double coded using a procedure informed by Charmaz's outline of grounded theory analysis and Morse's outline of the cognitive basis of qualitative research. RESULTS: In this article, we report on A. Hermes' interviews with members from the above Aboriginal communities, as well as on her personal views, experiences, and interpretations of the interviews she conducted with other community members. We found that participation in the NCIG biobank raised issues around broken trust, grief and loss, but also - somewhat unexpectedly - was perceived as a source of empowerment, hope and reconnection. CONCLUSIONS: This research reminds us (again) of the need to engage deeply with communities in order to respond appropriately with respect for their cultural values and norms, and to develop culturally relevant policies and processes that enhance the benefits of biobank participation and minimise potential harms.

Indigenous Genetics and Rare Diseases: Harmony, Diversity and Equity.

Advances in our understanding of genetic and rare diseases are changing the face of healthcare. Crucially, the global community must implement these advances equitably to reduce health disparities, including between Indigenous and non-Indigenous peoples. We take an Australian perspective to illustrate some key areas that are fundamental to the equitable translation of new knowledge for the improved diagnosis of genetic and rare diseases for Indigenous people. Specifically, we focus on inequalities in access to clinical genetics services and the lack of genetic and phenomic reference data to inform diagnoses. We provide examples of ways in which these inequities are being addressed through Australian partnerships to support a harmonious and inclusive approach to ensure that benefits from traditional wisdom, community knowledge and shared experiences are interwoven to support and inform implementation of new knowledge from genomics and precision public health. This will serve to deliver benefits to all of our diverse citizens, including Indigenous populations.

A Mutation in DAOA Modifies the Age of Onset in PSEN1 E280A Alzheimer's Disease.

We previously reported age of onset (AOO) modifier genes in the world's largest pedigree segregating early-onset Alzheimer's disease (AD), caused by the p.Glu280Ala (E280A) mutation in the PSEN1 gene. Here we report the results of a targeted analysis of functional exonic variants in those AOO modifier genes in sixty individuals with PSEN1 E280A AD who were whole-exome genotyped for ~250,000 variants. Standard quality control, filtering, and annotation for functional variants were applied, and common functional variants located in those previously reported as AOO modifier loci were selected. Multiloci linear mixed-effects models were used to test the association between these variants and AOO. An exonic missense mutation in the G72 (DAOA) gene (rs2391191, P = 1.94 × 10(-4), P FDR = 9.34 × 10(-3)) was found to modify AOO in PSEN1 E280A AD. Nominal associations of missense mutations in the CLUAP1 (rs9790, P = 7.63 × 10(-3), P FDR = 0.1832) and EXOC2 (rs17136239, P = 0.0325, P FDR = 0.391) genes were also found. Previous studies have linked polymorphisms in the DAOA gene with the occurrence of neuropsychiatric symptoms such as depression, apathy, aggression, delusions, hallucinations, and psychosis in AD. Our findings strongly suggest that this new conspicuous functional AOO modifier within the G72 (DAOA) gene could be pivotal for understanding the genetic basis of AD.

Mutations modifying sporadic Alzheimer's disease age of onset.

The identification of mutations modifying the age of onset (AOO) in Alzheimer's disease (AD) is crucial for understanding the natural history of AD and, therefore, for early interventions. Patients with sporadic AD (sAD) from a genetic isolate in the extremes of the AOO distribution were whole-exome genotyped. Single- and multi-locus linear mixed-effects models were used to identify functional variants modifying AOO. A posteriori enrichment and bioinformatic analyses were applied to evaluate the non-random clustering of the associate variants to physiopathological pathways involved in AD. We identified more than 20 pathogenic, genome-wide statistically significant mutations of major modifier effect on the AOO. These variants are harbored in genes implicated in neuron apoptosis, neurogenesis, inflammatory processes linked to AD, oligodendrocyte differentiation, and memory processes. This set of new genes harboring these mutations could be of importance for prediction, follow-up and eventually as therapeutical targets of AD. © 2016 Wiley Periodicals, Inc.

Hippocampal atrophy is associated with subjective memory decline: The PATH Through Life study.

OBJECTIVE: To investigate whether subjective memory decline (SMD) in cognitively healthy individuals is associated with hippocampal atrophy. METHODS: Multiple regression analyses assessing the relationship between hippocampal atrophy over 4 years and SMD at baseline and follow-up in 305 cognitively healthy individuals aged 60-64 years free from dementia, mild cognitive impairment, and other neurological disorders. RESULTS: SMD at baseline was not a significant predictor of hippocampal atrophy. However, SMD at follow-up was associated with greater hippocampal atrophy. Associations were reduced but remained significant after controlling for anxiety and depression symptomatology. CONCLUSION: Hippocampal atrophy was associated with incident/persisting SMD and this association was not, or only partly, explained by anxiety and depression symptomatology. These results are consistent with a biological origin to subjective memory decline. SMD should be included in screening and neuropsychological batteries.

Cognitive diversity and moral enhancement.

One debate in contemporary bioethics centers on whether the development of cognitive enhancement technologies (CETs) will hasten the need for moral enhancement. In this article we provide a new argument in favor of pursuing these enhancement technologies together. The widespread availability of CETs will likely increase population-level cognitive diversity. Different people will choose to enhance different aspects of their cognition, and some won't enhance themselves at all. Although this has the potential to be beneficial for society, it could also result in harms as people become more different from one another. Aspects of our moral psychology make it difficult for people to cooperate and coordinate actions with those who are very different from themselves. These moral failings could be targeted by moral enhancement technologies, which may improve cooperation among individuals. Moral enhancement technologies will therefore help society maximize the benefits, and reduce the costs, associated with widespread access to cognitive enhancements.

Long-term cognitive correlates of traumatic brain injury across adulthood and interactions with APOE genotype, sex, and age cohorts.

There is continuing debate about long-term effects of brain injury. We examined a range of traumatic brain injury (TBI) variables (TBI history, severity, frequency, and age of injury) as predictors of cognitive outcome over 8 years in an adult population, and interactions with apolipoprotein E (APOE) genotype, sex, and age cohorts. Three randomly sampled age cohorts (20-24, 40-44, 60-64 years at baseline; N = 6333) were each evaluated three times over 8 years. TBI variables, based on self-report, were separately modeled as predictors of cognitive performance using linear mixed effects models. TBI predicted longitudinal cognitive decline in all three age groups. APOE ε4 + genotypes in the young and middle-aged groups predicted lower baseline cognitive performance in the context of TBI. Baseline cognitive performance was better for young females than males but this pattern reversed in middle age and old age. The findings suggest TBI history is associated with long-term cognitive impairment and decline across the adult lifespan. A role for APOE genotype was apparent in the younger cohorts but there was no evidence that it is associated with impairment in early old age. The effect of sex and TBI on cognition varied with age cohort, consistent with a proposed neuroprotective role for estrogen.

An 1H-MRS framework predicts the onset of Alzheimer's disease symptoms in PSEN1 mutation carriers.

BACKGROUND: Alzheimer's disease (AD) is the most common cause of dementia; the main risk factors are age and several recently identified genes. A major challenge for AD research is the early detection of subjects at risk. The aim of this study is to develop a predictive model using proton magnetic resonance spectroscopy (1H-MRS), a noninvasive technique that evaluates brain chemistry in vivo, for monitoring the clinical outcome of carriers of a fully penetrant mutation that causes AD. METHODS: We studied 75 subjects from the largest multigenerational pedigree in the world (∼5000 people) that segregates a unique form of early-onset Alzheimer's disease (EOAD) caused by a fully penetrant mutation in the Presenilin-1 gene (PSEN1 p.Glu280Ala [E280 A]). Forty-four subjects were carriers of the mutation, and 31 were noncarriers. Seventeen carriers had either mild cognitive impairment (MCI) or early-stage AD (collectively MCI-AD). In right and left parietal white mater and parasagittal parietal gray matter (RPPGM and LPPGM) of the posterior cingulate gyrus and precuneus, we measured levels of the brain metabolites N-acetylaspartate (NAA), inositol (Ins), choline (Cho), and glutamate-glutamine complex (Glx) relative to creatine (Cr) levels (NAA/Cr, Ins/Cr, Cho/Cr, and Glx/Cr, respectively) with two-dimensional 1H-MRS. Using advanced recursive partition analysis and random forest analysis, we built classificatory decision trees for both mutation carrier status and the presence of MCI-AD symptoms, fitting them to 1H-MRS data while controlling for age, educational level, and sex. RESULTS: We found that (1) the combination of LPPGM Cho/Cr<0.165 and RPPGM Glx/Cr>1.54 fully excluded carriers; (2) LPPGM Cho/Cr>0.165, RPPGM Glx/Cr<1.54, and left parietal white mater NAA/Cr>1.16 identified asymptomatic carriers with sensitivity of 97.7% and specificity of 77.4%; and (3) RPPGM NAA/Cr>1.05 defined asymptomatic subjects (independent of carrier status) with sensitivity of 100% and a specificity of 96.6%. CONCLUSIONS: Brain metabolites measured by 1H-MRS in the posterior cingulate gyrus and precuneus are optimally sensitive and specific potential noninvasive biomarkers of subclinical emergence of AD caused by the PSEN1 p.Glu280Ala (E280 A) mutation.

Predicting the presence of hepatitis B virus surface antigen in Chinese patients by pathology data mining.

Hepatitis B virus (HBV) is a pathogen of worldwide health significance, associated with liver disease. A vaccine is available, yet HBV prevalence remains a concern, particularly in developing countries. Pathology laboratories have a primary role in the diagnosis and monitoring of HBV infection, through hepatitis B surface antigen (HBsAg) immunoassay and associated tests. Analysis of HBsAg immunoassay and associated pathology data from 821 Chinese patients applied 10-fold cross-validation to establish classification decision trees (CDTs), with CDT results used subsequently to develop a logistic regression model. The robustness of logistic regression model was confirmed by the Hosmer-Lemeshow test, Pseudo-R(2) and an area under receiver operating characteristic curve (AUROC) result that showed the logistic regression model was capable of accurately discriminating the HBsAg positive from HBsAg negative patients at 95% accuracy. Overall CDT sensitivity and specificity was 94.7% (± 5.0%) and 89.5% (± 5.7%), respectively, close to the sensitivity and specificity of the immunoassay, providing an alternative to predict HBsAg status. Both the CDT and logistic regression modeling demonstrated the importance of the routine pathology variables alanine aminotransferase (ALT), serum albumin (ALB), and alkaline phosphatase (ALP) to accurately predict HBsAg status in a Chinese patient cohort. The study demonstrates that CDTs and a linked logistic regression model applied to routine pathology data were an effective supplement to HBsAg immunoassay, and a possible replacement method where immunoassays are not requested or not easily available for the laboratory diagnosis of HBV infection.

Characterizing mild cognitive disorders in the young-old over 8 years: prevalence, estimated incidence, stability of diagnosis, and impact on IADLs.

OBJECTIVES: Few studies report incidence of mild cognitive impairment (MCI) and other mild cognitive disorders (MCD) in cohorts in their 60s, at an age when diagnoses are less stable. The authors' goal was to estimate the incidence and prevalence of MCI and MCD, characterize subgroups with stable vs nonstable diagnoses, and evaluate the impact of diagnosis on daily life in a young-old cohort. METHODS: A community-based cohort age 60 to 64 years in 1999 (n = 2551) was monitored for 8 years and assessed every 4 years. A two-stage sampling design was used to identify MCI and MCD through a neuropsychological and neurological assessment. A panel of physicians blind to previous diagnoses reviewed each case using published criteria. RESULTS: The prevalence of MCDs in the cohort aged 68 to 72 years at the last follow-up was approximately 10%. An estimated 141 subjects (7.7%) progressed to MCI and 183 subjects (10.0%) progressed to MCD between years 4 and 8. Only eight participants received a dementia diagnosis at any wave, five of whom progressed from MCDs. More than 45% of diagnoses were unstable during the 8 years of follow-up. Stable diagnoses were associated with lower Mini-Mental State Examination scores, history of neurological disorder, higher cardiovascular risk, and depression at baseline. MCDs were associated with impairments in instrumental activities of daily living and higher rates of reporting memory problems prior to diagnosis. CONCLUSIONS: MCDs in individuals in their 60s occur in at least 10% of the population and are likely to be heterogeneous in terms of their etiology and long-term prognosis, but may cause a significant impact in everyday life.

Self-reported cognitive decline on the informant questionnaire on cognitive decline in the elderly is associated with dementia, instrumental activities of daily living and depression but not longitudinal cognitive change.

BACKGROUND/AIM: A subjective history of cognitive decline is integral to dementia screening, yet there are few data on the accuracy of retrospective self-reports. We prospectively examined the longitudinal predictors of self-reported decline, including rate of cognitive change, clinical diagnosis, depressive symptoms and personality. METHODS: We used a large (n = 2,551) community-dwelling sample of older adults (60-64 years at baseline) and tracked their cognitive functioning over 3 waves across a period of 8 years. Individual rates of change in multiple domains of cognition, incident dementia and mild cognitive disorders, apolipoprotein E (APOE) ε4 genotype, level of education, depressive symptoms and personality were examined as predictors of wave 3 retrospective self-reported decline as measured by the Informant Questionnaire on Cognitive Decline in the Elderly. RESULTS: The rate of cognitive decline did not predict subjective decline. Significant predictors of self-reported decline included dementia diagnosis, problems with instrumental activities of daily living, depression and neuroticism at the time of self-report, as well as the presence of an APOE ε4 allele. CONCLUSIONS: In this relatively young cohort, retrospective self-report of cognitive decline does not reflect objective deterioration in cognition over the time period in question, but it may identify individuals in the initial stages of dementia and those with elevated psychological and genotypic risk factors for the development of dementia.

Lifetime cigarette smoking is associated with striatal volume measures.

Nicotine, the primary addictive component of tobacco, affects the mammalian brain. Smokers' brains have smaller cortical grey matter volumes and/or lower densities compared with non-smokers'. Differences in subcortical structures like the striatum are however, less clear. A high concentration of nicotinic receptors makes the striatum a potential target for nicotine. In addition, striatal nuclei are essential components of the reward/reinforcement pathway involved in addiction. The aim of this study was to explore the relationship between striatal nuclei (caudate, putamen and nucleus accumbens area) volumes and lifetime smoking in a large community-based sample of 'young-old' individuals. Brain volumes were measured using a semi-automated method in 315 participants aged 64-70 years who were selected from a larger randomly sampled cohort and who consented to a magnetic resonance imaging scan. Multiple regression analysis was used to assess the relationship between striatal volumes and cigarette smoking measures while controlling for age, sex, intracranial and total brain volumes and general physical and mental health measures. Greater lifetime use of cigarettes (measured in pack-years) was associated with smaller left nucleus accumbens area volume (P = 0.018) and larger left putamen volume (P = 0.025). Greater putaminal volume was also associated with a lower age at smoking initiation (P = 0.004). In this generally healthy cohort, lifetime use of cigarettes is significantly associated with striatal volume measures. These changes could indicate predisposing factors for nicotine addiction, or an effect of chronic nicotine exposure or a combination of both.

Estimates of the effect of natural selection on protein-coding content.

Analysis of natural selection is key to understanding many core biological processes, including the emergence of competition, cooperation, and complexity, and has important applications in the targeted development of vaccines. Selection is hard to observe directly but can be inferred from molecular sequence variation. For protein-coding nucleotide sequences, the ratio of nonsynonymous to synonymous substitutions (omega) distinguishes neutrally evolving sequences (omega = 1) from those subjected to purifying (omega < 1) or positive Darwinian (omega > 1) selection. We show that current models used to estimate omega are substantially biased by naturally occurring sequence compositions. We present a novel model that weights substitutions by conditional nucleotide frequencies and which escapes these artifacts. Applying it to the genomes of pathogens causing malaria, leprosy, tuberculosis, and Lyme disease gave significant discrepancies in estimates with approximately 10-30% of genes affected. Our work has substantial implications for how vaccine targets are chosen and for studying the molecular basis of adaptive evolution.

Effect of model choice in genetic association studies: DRD4 exon III VNTR and cigarette use in young adults.

A major concern with the vast literature associating the highly polymorphic 48 bp VNTR in exon III of the human dopamine receptor D4 gene (DRD4) with various behavioral phenotypes is the lack of concordance between studies. Part of the problem arises from the absence of a universally accepted scheme for pooling the large number of low frequency genotypes into appropriate categories. Here, we investigated the effect of different pooling strategies and genetic models on the reported association between DRD4-exIII-VNTR polymorphism and cigarette smoking. Genotyping was performed on a large randomly selected community-based sample of 2,274 individuals aged 20-24 years. Participants were grouped into sub-samples based on their genotypes to test specific genetic models. Multiple regression analyses were used to assess the relationship between DRD4-exIII-VNTR genotype and cigarette smoking measures while controlling for confounders. While smoking status and age at start of smoking were not associated with the genotype, a significantly (P = 0.006) higher rate of cigarette consumption was observed among carriers of the 7-repeat (7r) allele. Thus, 7r carriers were not more likely to be smokers but if they did smoke they consumed significantly more cigarettes per day than 4r carriers. Unlike previous studies this association was observed only when comparing carriers of the 7r with the 4r but not the other repeat alleles. Our study demonstrates the need for caution when grouping functionally different DRD4-exIII-VNTR alleles in association studies. It particularly highlights the requirement for better functional characterization of the DRD4-exIII-VNTR alleles for interpreting results from association studies.

Mitochondrial pathway polygenic risk scores are associated with Alzheimer's Disease.

Genetic, animal and epidemiological studies involving biomolecular and clinical endophenotypes implicate mitochondrial dysfunction in Alzheimer's disease (AD) pathogenesis. Polygenic risk scores (PRS) provide a novel approach to assess biological pathway-associated disease risk by combining the effects of variation at multiple, functionally related genes. We investigated the associations of PRS for genes involved in 12 mitochondrial pathways (pathway-PRS) with AD in 854 participants from Alzheimer's Disease Neuroimaging Initiative. Pathway-PRS for the nuclear-encoded mitochondrial genome (OR: 1.99 [95% Cl: 1.70, 2.35]) and three mitochondrial pathways is significantly associated with increased AD risk: (i) response to oxidative stress (OR: 2.01 [95% Cl: 1.71, 2.38]); (ii) mitochondrial transport (OR: 1.81 [95% Cl: 1.55, 2.13]); (iii) hallmark oxidative phosphorylation (OR: 1.22 [95% Cl: 1.06, 1.40]. Therapeutic approaches targeting these pathways may have the potential for modifying AD pathogenesis. Further investigation is required to establish a causal role for these pathways in AD pathology.