Rare coding variants in PLCG2, ABI3, and TREM2 implicate microglial-mediated innate immunity in Alzheimer's disease

We identified rare coding variants associated with Alzheimer’s disease (AD) in a 3-stage case-control study of 85,133 subjects. In stage 1, 34,174 samples were genotyped using a whole-exome microarray. In stage 2, we tested associated variants (P<1×10-4) in 35,962 independent samples using de novo genotyping and imputed genotypes. In stage 3, an additional 14,997 samples were used to test the most significant stage 2 associations (P<5×10-8) using imputed genotypes. We observed 3 novel genome-wide significant (GWS) AD associated non-synonymous variants; a protective variant in PLCG2 (rs72824905/p.P522R, P=5.38×10-10, OR=0.68, MAFcases=0.0059, MAFcontrols=0.0093), a risk variant in ABI3 (rs616338/p.S209F, P=4.56×10-10, OR=1.43, MAFcases=0.011, MAFcontrols=0.008), and a novel GWS variant in TREM2 (rs143332484/p.R62H, P=1.55×10-14, OR=1.67, MAFcases=0.0143, MAFcontrols=0.0089), a known AD susceptibility gene. These protein-coding changes are in genes highly expressed in microglia and highlight an immune-related protein-protein interaction network enriched for previously identified AD risk genes. These genetic findings provide additional evidence that the microglia-mediated innate immune response contributes directly to AD development

Differences in Preferences for Models of Consent for Biobanks Between Black and White Women

Biobanks are essential resources, and participation by individuals from diverse groups is needed. Various models of consent have been proposed for secondary research use of biospecimens, differing in level of donor control and information received. Data are needed regarding participant preferences for models of consent, particularly among minorities. We conducted qualitative semi-structured interviews with 60 women to examine their attitudes about different models of consent. Recruitment was stratified by race (Black/White) and prior biobank participation (yes/no). Two coders independently coded interview transcripts. Qualitative thematic analysis was conducted using NVivo 10. The majority of Black and White participants preferred “broad” consent (i.e., blanket permission for secondary research use of biospecimens), and the second most preferred model for both groups was “study-specific” consent (i.e., consent for each future research study). The qualitative analysis showed that participants selected their most preferred model for 3 major reasons: having enough information, having control over their sample, and being asked for permission. Least preferred was notice model (i.e., participants notified that biospecimens may be used in future research). Attitudes toward models of consent differed somewhat by race and prior biobank participation. Participants preferred models of consent for secondary research use of biospecimens that provided them with both specific and general information, control over their biospecimens, and asked them to give permission for use. Our findings suggest that it will be important for researchers to provide information about future uses of biospecimens to the extent possible and have an explicit permission step for secondary research use

Differences in Preferences for Models of Consent for Biobanks Between Black and White Women

Biobanks are essential resources, and participation by individuals from diverse groups is needed. Various models of consent have been proposed for secondary research use of biospecimens, differing in level of donor control and information received. Data are needed regarding participant preferences for models of consent, particularly among minorities. We conducted qualitative semi-structured interviews with 60 women to examine their attitudes about different models of consent. Recruitment was stratified by race (Black/White) and prior biobank participation (yes/no). Two coders independently coded interview transcripts. Qualitative thematic analysis was conducted using NVivo 10. The majority of Black and White participants preferred “broad” consent (i.e., blanket permission for secondary research use of biospecimens), and the second most preferred model for both groups was “study-specific” consent (i.e., consent for each future research study). The qualitative analysis showed that participants selected their most preferred model for 3 major reasons: having enough information, having control over their sample, and being asked for permission. Least preferred was notice model (i.e., participants notified that biospecimens may be used in future research). Attitudes toward models of consent differed somewhat by race and prior biobank participation. Participants preferred models of consent for secondary research use of biospecimens that provided them with both specific and general information, control over their biospecimens, and asked them to give permission for use. Our findings suggest that it will be important for researchers to provide information about future uses of biospecimens to the extent possible and have an explicit permission step for secondary research use

Association of the ADAM33 gene with asthma and bronchial hyperresponsiveness

Asthma is a common respiratory disorder characterized by recurrent episodes of coughing, wheezing and breathlessness. Although environmental factors such as allergen exposure are risk factors in the development of asthma, both twin and family studies point to a strong genetic component. To date, linkage studies have identified more than a dozen genomic regions linked to asthma. In this study, we performed a genome-wide scan on 460 Caucasian families and identified a locus on chromosome 20p13 that was linked to asthma (log10 of the likelihood ratio (LOD), 2.94) and bronchial hyperresponsiveness (LOD, 3.93). A survey of 135 polymorphisms in 23 genes identified the ADAM33 gene as being significantly associated with asthma using case-control, transmission disequilibrium and haplotype analyses (P = 0.04?0.000003). ADAM proteins are membrane-anchored metalloproteases with diverse functions, which include the shedding of cell-surface proteins such as cytokines and cytokine receptors. The identification and characterization of ADAM33, a putative asthma susceptibility gene identified by positional cloning in an outbred population, should provide insights into the pathogenesis and natural history of this common disease

Complete Genome Sequence of Methanobacterium thermoautotrophicum &amp;Delta;H: Functional . . .

the ORF-encoded polypeptides are related to sequences with unknown functions, and 496 (27%) have little or no homology to sequences in public databases. Comparisons with Eucarya-, Bacteria-, and Archaea -specific databases reveal that 1,013 of the putative gene products (54%) are most similar to polypeptide sequences described previously for other organisms in the domain Archaea. Comparisons with the Methanococcus jannaschii genome data underline the extensive divergence that has occurred between these two methanogens; only 352 (19%) of M. thermoautotrophicum ORFs encode sequences that are &gt;50% identical to M. jannaschii polypeptides, and there is little conservation in the relative locations of orthologous genes. When the M. thermoautotrophicum ORFs are compared to sequences from only the eucaryal and bacterial domains, 786 (42%) are more similar to bacterial sequences and 241 (13%) are more similar to eucaryal sequences. The bacterial domain-like gene products include the m