Genetic and neurophysiological correlates of the age of onset of alcohol use disorders in adolescents and young adults.

Discrete time survival analysis was used to assess the age-specific association of event-related oscillations (EROs) and CHRM2 gene variants on the onset of regular alcohol use and alcohol dependence. The subjects were 2,938 adolescents and young adults ages 12-25. Results showed that the CHRM2 gene variants and ERO risk factors had hazards which varied considerably with age. The bulk of the significant age-specific associations occurred in those whose age of onset was under 16. These associations were concentrated in those subjects who at some time took an illicit drug. These results are consistent with studies which associate greater rates of alcohol dependence among those who begin drinking at an early age. The age specificity of the genetic and neurophysiological factors is consistent with recent studies of adolescent brain development, which locate an interval of heightened vulnerability to substance use disorders in the early to mid teens

Rare X-linked variants carry predominantly male risk in autism, Tourette syndrome, and ADHD

© The Author(s) 2023. Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.Autism spectrum disorder (ASD), Tourette syndrome (TS), and attention-deficit/hyperactivity disorder (ADHD) display strong male sex bias, due to a combination of genetic and biological factors, as well as selective ascertainment. While the hemizygous nature of chromosome X (Chr X) in males has long been postulated as a key point of “male vulnerability”, rare genetic variation on this chromosome has not been systematically characterized in large-scale whole exome sequencing studies of “idiopathic” ASD, TS, and ADHD. Here, we take advantage of informative recombinations in simplex ASD families to pinpoint risk-enriched regions on Chr X, within which rare maternally-inherited damaging variants carry substantial risk in males with ASD. We then apply a modified transmission disequilibrium test to 13,052 ASD probands and identify a novel high confidence ASD risk gene at exome-wide significance (MAGEC3). Finally, we observe that rare damaging variants within these risk regions carry similar effect sizes in males with TS or ADHD, further clarifying genetic mechanisms underlying male vulnerability in multiple neurodevelopmental disorders that can be exploited for systematic gene discovery.This study was supported by grants from the National Institute of Mental Health to A.J.W. and M.W.S (R01MH115963), A.J.W. (R01NS105746), G.A.H. and J.A.T. (R01MH115958), Alyssa Rosen (R01MH115960), Donald L. Gilbert (R01MH115962), Samuel Kuperman (R01MH115961), Samuel H. Zinner (R01MH115993), Barbara J. Coffey (R01MH115959), B.W. (R25MH06048); from the Tourette Association of America to A.J.W. (Young Investigator Award); from the Human Genetics Institute of New Jersey to G.A.H. and J.A.T.; and the New Jersey Center for Tourette Syndrome and Associated Disorders (NJCTS) to G.A.H. and J.A.T.Peer reviewe

Concept, Design and Implementation of a Cardiovascular Gene-Centric 50 K SNP Array for Large-Scale Genomic Association Studies

A wealth of genetic associations for cardiovascular and metabolic phenotypes in humans has been accumulating over the last decade, in particular a large number of loci derived from recent genome wide association studies (GWAS). True complex disease-associated loci often exert modest effects, so their delineation currently requires integration of diverse phenotypic data from large studies to ensure robust meta-analyses. We have designed a gene-centric 50 K single nucleotide polymorphism (SNP) array to assess potentially relevant loci across a range of cardiovascular, metabolic and inflammatory syndromes. The array utilizes a “cosmopolitan” tagging approach to capture the genetic diversity across ∼2,000 loci in populations represented in the HapMap and SeattleSNPs projects. The array content is informed by GWAS of vascular and inflammatory disease, expression quantitative trait loci implicated in atherosclerosis, pathway based approaches and comprehensive literature searching. The custom flexibility of the array platform facilitated interrogation of loci at differing stringencies, according to a gene prioritization strategy that allows saturation of high priority loci with a greater density of markers than the existing GWAS tools, particularly in African HapMap samples. We also demonstrate that the IBC array can be used to complement GWAS, increasing coverage in high priority CVD-related loci across all major HapMap populations. DNA from over 200,000 extensively phenotyped individuals will be genotyped with this array with a significant portion of the generated data being released into the academic domain facilitating in silico replication attempts, analyses of rare variants and cross-cohort meta-analyses in diverse populations. These datasets will also facilitate more robust secondary analyses, such as explorations with alternative genetic models, epistasis and gene-environment interactions

Meiotic Recombination Initiation in and around Retrotransposable Elements in <i>Saccharomyces cerevisiae</i>

<div><p>Meiotic recombination is initiated by large numbers of developmentally programmed DNA double-strand breaks (DSBs), ranging from dozens to hundreds per cell depending on the organism. DSBs formed in single-copy sequences provoke recombination between allelic positions on homologous chromosomes, but DSBs can also form in and near repetitive elements such as retrotransposons. When they do, they create a risk for deleterious genome rearrangements in the germ line via recombination between non-allelic repeats. A prior study in budding yeast demonstrated that insertion of a Ty retrotransposon into a DSB hotspot can suppress meiotic break formation, but properties of Ty elements in their most common physiological contexts have not been addressed. Here we compile a comprehensive, high resolution map of all Ty elements in the rapidly and efficiently sporulating <i>S. cerevisiae</i> strain SK1 and examine DSB formation in and near these endogenous retrotransposable elements. SK1 has 30 Tys, all but one distinct from the 50 Tys in S288C, the source strain for the yeast reference genome. From whole-genome DSB maps and direct molecular assays, we find that DSB levels and chromatin structure within and near Tys vary widely between different elements and that local DSB suppression is not a universal feature of Ty presence. Surprisingly, deletion of two Ty elements weakened adjacent DSB hotspots, revealing that at least some Ty insertions promote rather than suppress nearby DSB formation. Given high strain-to-strain variability in Ty location and the high aggregate burden of Ty-proximal DSBs, we propose that meiotic recombination is an important component of host-Ty interactions and that Tys play critical roles in genome instability and evolution in both inbred and outcrossed sexual cycles.</p></div

Chromatin structures of Ty elements.

<p>(A) Preferential MNase cleavage of chromatin in nucleosome-depleted regions (NDR) and linkers between nucleosomes. (B–C) MNase sensitivity of regions in and around Ty<i>_CGR1-SCW11</i> (B) and Ty<i>_PEX25-CAR1</i> (C). Intact meiotic nuclei were treated with 0, 2.5×10⁻⁵, or 5×10⁻⁵ units of MNase per µg of DNA (lanes 1–3) and purified genomic DNA (N, for naked DNA) from vegetative cells was treated with 1.6×10⁻⁴ units per µg DNA (lane 4), then MNase cleavage patterns were determined by Southern blotting and indirect end-labeling. Genomic DNA prepared from meiotic <i>sae2Δ</i> cells is a marker for DSB positions (lane 5). Profiles of lanes 1 (−MNase), 3 (+MNase), and 5 (DSBs) are shown to the right of each blot. Red bars on ORF maps indicate probe positions.</p

Location of Ty elements in SK1.

<p>The insertion sites and orientations of SK1 Ty elements are shown in comparison to S288C Tys (chromosomal coordinates are from S288C). Fragmented arrowheads indicate partial Ty elements. Open circles show centromeres. Dashed circle highlights the only Ty shared between the two strains.</p

Location of Ty elements in SK1.

a<p>The coordinates of Ty insertion sites are based on the S288C reference genome (the June 2008 assembly from the Saccharomyces Genome Database). When a Ty insertion site exhibits a 5-bp duplication, the third and fourth bp are used as the start and end coordinates, respectively.</p>b<p>Although the family of Ty<i>_URA3</i> and Ty<i>_YER137C-RTR1</i> could not be determined by established criteria <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003732#pgen.1003732-Kim1" target="_blank">[11]</a> (<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003732#pgen.1003732.s001" target="_blank">Figure S1D</a>), these Tys were classified as Ty1 by Gabriel et al. (2006).</p>c<p>The presence (+) or absence (−) of tRNA in the same intergenic region with a Ty is indicated.</p>d<p>The target site sequence duplicated on the same strand with a Ty is indicated. N.D. indicates that the presence or absence of sequence duplication was not determined. “–” indicates that sequence duplication was not observed.</p>e<p>Ty element is inserted in a novel SK1 LTR. The insertion site of the LTR is indicated.</p>f<p>Ty<i>_{YBL108W-YBL107C}</i> and Ty<i>_{TEL03L-YCL073C}</i> are located in subtelomeric regions, which are enriched with repeated sequences and are dynamic among strains <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003732#pgen.1003732-Louis1" target="_blank">[65]</a>. Since chromosome ends are not well defined in the SK1 genome assembly, it remains to be determined which chromosome end(s) carry these Tys.</p>g<p>Ty<i>_{TEL03L-YCL073C}</i> is the same as <i>YCLWTy5-1</i> in S288C.</p>h<p>A full-length Ty<i>_{EXG2-YDR262W-1}</i> and a fragmented Ty<i>_{EXG2-YDR262W-2}</i> of >1 kb in size are located adjacent to each other.</p>i<p>Ty<i>_OMS1-HIM1</i> is a ∼1-kb fragmented Ty.</p>j<p>Ty_{NCE103-YNL035C-1} is disrupted by Ty_{NCE103-YNL035C-2}.</p

Meiotic DSBs in and around Ty elements.

<p>(A) Spo11 oligo densities around Ty elements. For each SK1 Ty, Spo11 oligo densities (hits per million mapped reads (hpM) per kb) were determined in the indicated window of adjacent sequence. Sites where Tys are present in S288C but absent in SK1 serve as controls. Bars are means and standard deviations; the dashed line is the genome average; p values are from Wilcoxon rank sum tests. For comparison, the internal Spo11 oligo density averaged across all Ty elements was 6.7 hpM/kb, approximately 30–40-fold lower than the mean for these flanking regions. (B) Spo11 oligo densities around Ty elements in different types of intergenic regions. (C–F) Physical detection of DSBs. (Left) Spo11 oligo distribution from Pan et al. (2011) and maps of ORFs (blue-filled polygons) and tRNA genes (horizontal bars). (Right) Southern blots of genomic DNA isolated from <i>spo11-Y135F</i>, <i>sae2Δ</i> and <i>dmc1Δ</i> strains at 6 hrs after entry into meiosis. Red numbers are DSB frequencies within the bracketed regions in each lane (% of total hybridization signal in the lane); quantification is provided separately for each lane, representing independent cultures. Red bars, probe positions; P, unbroken (parental) restriction fragments; asterisks, cross hybridizing bands. Flanking restriction sites plus internal sites used to generate genomic DNA markers (run on the same gels; not shown) are indicated: NcoI (N), BsaXI (XI), PpuMI (MI), Bsu36I (Bs), BglII (Bg), BspHI (HI), BamHI (B), ApaLI (Ap), SnaBI (Sn), NdeI (Nd). In (F), the inset shows a more exposed contrast of the phosphorimager signal for the region indicated by the dashed line. (G) Quantitative agreement between Spo11 oligo counts and DSB frequencies at hotspots near Ty elements in <i>dmc1Δ</i> mutants. DSB values are the means of the two independent cultures shown in panels C–F.</p

Deleting Ty elements increases DSB formation nearby.

<p>(A–D) Genomic DNA was isolated from meiotic cultures of a <i>dmc1Δ</i> strain containing the full complement of SK1 Tys and <i>dmc1Δ</i> strains in which either Ty<i>_EST3-FAA3</i> or Ty<i>_CGR1-SCW11</i> was deleted. DSBs were detected by Southern blotting and indirect end-labeling. Figures are labeled as in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003732#pgen-1003732-g004" target="_blank">Figures 4C–F</a>. Circled lower case roman numerals indicate hotspots discussed in the text. Red numerals are DSB frequencies within the bracketed regions in each of two independent cultures, corrected where appropriate for differences in transfer efficiency for the parental fragments (see <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003732#s4" target="_blank">Materials and Methods</a>). Blots were stripped and rehybridized to probes from separate loci to serve as loading controls (lower panels). (A,B) DSBs around the Ty<i>_EST3-FAA3</i> insertion site, probed from either side. (C,D) DSBs around the Ty<i>_CGR1-SCW11</i> insertion site, probed from either side. (E) DSBs at the <i>YCR048W</i> hotspot (control locus) in the same samples as in panels A–D.</p